Science.gov

Sample records for advanced multi-scale modeling

  1. Advances in multi-scale modeling of solidification and casting processes

    NASA Astrophysics Data System (ADS)

    Liu, Baicheng; Xu, Qingyan; Jing, Tao; Shen, Houfa; Han, Zhiqiang

    2011-04-01

    The development of the aviation, energy and automobile industries requires an advanced integrated product/process R&D systems which could optimize the product and the process design as well. Integrated computational materials engineering (ICME) is a promising approach to fulfill this requirement and make the product and process development efficient, economic, and environmentally friendly. Advances in multi-scale modeling of solidification and casting processes, including mathematical models as well as engineering applications are presented in the paper. Dendrite morphology of magnesium and aluminum alloy of solidification process by using phase field and cellular automaton methods, mathematical models of segregation of large steel ingot, and microstructure models of unidirectionally solidified turbine blade casting are studied and discussed. In addition, some engineering case studies, including microstructure simulation of aluminum casting for automobile industry, segregation of large steel ingot for energy industry, and microstructure simulation of unidirectionally solidified turbine blade castings for aviation industry are discussed.

  2. Advanced computational workflow for the multi-scale modeling of the bone metabolic processes.

    PubMed

    Dao, Tien Tuan

    2016-09-16

    Multi-scale modeling of the musculoskeletal system plays an essential role in the deep understanding of complex mechanisms underlying the biological phenomena and processes such as bone metabolic processes. Current multi-scale models suffer from the isolation of sub-models at each anatomical scale. The objective of this present work was to develop a new fully integrated computational workflow for simulating bone metabolic processes at multi-scale levels. Organ-level model employs multi-body dynamics to estimate body boundary and loading conditions from body kinematics. Tissue-level model uses finite element method to estimate the tissue deformation and mechanical loading under body loading conditions. Finally, cell-level model includes bone remodeling mechanism through an agent-based simulation under tissue loading. A case study on the bone remodeling process located on the human jaw was performed and presented. The developed multi-scale model of the human jaw was validated using the literature-based data at each anatomical level. Simulation outcomes fall within the literature-based ranges of values for estimated muscle force, tissue loading and cell dynamics during bone remodeling process. This study opens perspectives for accurately simulating bone metabolic processes using a fully integrated computational workflow leading to a better understanding of the musculoskeletal system function from multiple length scales as well as to provide new informative data for clinical decision support and industrial applications.

  3. Advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models

    PubMed Central

    Barberis, Matteo; Todd, Robert G.; van der Zee, Lucas

    2016-01-01

    The eukaryotic cell cycle is robustly designed, with interacting molecules organized within a definite topology that ensures temporal precision of its phase transitions. Its underlying dynamics are regulated by molecular switches, for which remarkable insights have been provided by genetic and molecular biology efforts. In a number of cases, this information has been made predictive, through computational models. These models have allowed for the identification of novel molecular mechanisms, later validated experimentally. Logical modeling represents one of the youngest approaches to address cell cycle regulation. We summarize the advances that this type of modeling has achieved to reproduce and predict cell cycle dynamics. Furthermore, we present the challenge that this type of modeling is now ready to tackle: its integration with intracellular networks, and its formalisms, to understand crosstalks underlying systems level properties, ultimate aim of multi-scale models. Specifically, we discuss and illustrate how such an integration may be realized, by integrating a minimal logical model of the cell cycle with a metabolic network. PMID:27993914

  4. Advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models.

    PubMed

    Barberis, Matteo; Todd, Robert G; van der Zee, Lucas

    2017-01-01

    The eukaryotic cell cycle is robustly designed, with interacting molecules organized within a definite topology that ensures temporal precision of its phase transitions. Its underlying dynamics are regulated by molecular switches, for which remarkable insights have been provided by genetic and molecular biology efforts. In a number of cases, this information has been made predictive, through computational models. These models have allowed for the identification of novel molecular mechanisms, later validated experimentally. Logical modeling represents one of the youngest approaches to address cell cycle regulation. We summarize the advances that this type of modeling has achieved to reproduce and predict cell cycle dynamics. Furthermore, we present the challenge that this type of modeling is now ready to tackle: its integration with intracellular networks, and its formalisms, to understand crosstalks underlying systems level properties, ultimate aim of multi-scale models. Specifically, we discuss and illustrate how such an integration may be realized, by integrating a minimal logical model of the cell cycle with a metabolic network.

  5. A framework for multi-scale modelling

    PubMed Central

    Chopard, B.; Borgdorff, Joris; Hoekstra, A. G.

    2014-01-01

    We review a methodology to design, implement and execute multi-scale and multi-science numerical simulations. We identify important ingredients of multi-scale modelling and give a precise definition of them. Our framework assumes that a multi-scale model can be formulated in terms of a collection of coupled single-scale submodels. With concepts such as the scale separation map, the generic submodel execution loop (SEL) and the coupling templates, one can define a multi-scale modelling language which is a bridge between the application design and the computer implementation. Our approach has been successfully applied to an increasing number of applications from different fields of science and technology. PMID:24982249

  6. Multi-scale modeling in cell biology

    PubMed Central

    Meier-Schellersheim, Martin; Fraser, Iain D. C.; Klauschen, Frederick

    2009-01-01

    Biomedical research frequently involves performing experiments and developing hypotheses that link different scales of biological systems such as, for instance, the scales of intracellular molecular interactions to the scale of cellular behavior and beyond to the behavior of cell populations. Computational modeling efforts that aim at exploring such multi-scale systems quantitatively with the help of simulations have to incorporate several different simulation techniques due to the different time and space scales involved. Here, we provide a non-technical overview of how different scales of experimental research can be combined with the appropriate computational modeling techniques. We also show that current modeling software permits building and simulating multi-scale models without having to become involved with the underlying technical details of computational modeling. PMID:20448808

  7. Multi-scaling modelling in financial markets

    NASA Astrophysics Data System (ADS)

    Liu, Ruipeng; Aste, Tomaso; Di Matteo, T.

    2007-12-01

    In the recent years, a new wave of interest spurred the involvement of complexity in finance which might provide a guideline to understand the mechanism of financial markets, and researchers with different backgrounds have made increasing contributions introducing new techniques and methodologies. In this paper, Markov-switching multifractal models (MSM) are briefly reviewed and the multi-scaling properties of different financial data are analyzed by computing the scaling exponents by means of the generalized Hurst exponent H(q). In particular we have considered H(q) for price data, absolute returns and squared returns of different empirical financial time series. We have computed H(q) for the simulated data based on the MSM models with Binomial and Lognormal distributions of the volatility components. The results demonstrate the capacity of the multifractal (MF) models to capture the stylized facts in finance, and the ability of the generalized Hurst exponents approach to detect the scaling feature of financial time series.

  8. Multi-scale models for cell adhesion

    NASA Astrophysics Data System (ADS)

    Wu, Yinghao; Chen, Jiawen; Xie, Zhong-Ru

    2014-03-01

    The interactions of membrane receptors during cell adhesion play pivotal roles in tissue morphogenesis during development. Our lab focuses on developing multi-scale models to decompose the mechanical and chemical complexity in cell adhesion. Recent experimental evidences show that clustering is a generic process for cell adhesive receptors. However, the physical basis of such receptor clustering is not understood. We introduced the effect of molecular flexibility to evaluate the dynamics of receptors. By delivering new theory to quantify the changes of binding free energy in different cellular environments, we revealed that restriction of molecular flexibility upon binding of membrane receptors from apposing cell surfaces (trans) causes large entropy loss, which dramatically increases their lateral interactions (cis). This provides a new molecular mechanism to initialize receptor clustering on the cell-cell interface. By using the subcellular simulations, we further found that clustering is a cooperative process requiring both trans and cis interactions. The detailed binding constants during these processes are calculated and compared with experimental data from our collaborator's lab.

  9. Multi-scale modeling for sustainable chemical production.

    PubMed

    Zhuang, Kai; Bakshi, Bhavik R; Herrgård, Markus J

    2013-09-01

    With recent advances in metabolic engineering, it is now technically possible to produce a wide portfolio of existing petrochemical products from biomass feedstock. In recent years, a number of modeling approaches have been developed to support the engineering and decision-making processes associated with the development and implementation of a sustainable biochemical industry. The temporal and spatial scales of modeling approaches for sustainable chemical production vary greatly, ranging from metabolic models that aid the design of fermentative microbial strains to material and monetary flow models that explore the ecological impacts of all economic activities. Research efforts that attempt to connect the models at different scales have been limited. Here, we review a number of existing modeling approaches and their applications at the scales of metabolism, bioreactor, overall process, chemical industry, economy, and ecosystem. In addition, we propose a multi-scale approach for integrating the existing models into a cohesive framework. The major benefit of this proposed framework is that the design and decision-making at each scale can be informed, guided, and constrained by simulations and predictions at every other scale. In addition, the development of this multi-scale framework would promote cohesive collaborations across multiple traditionally disconnected modeling disciplines to achieve sustainable chemical production.

  10. Microphysics in Multi-scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2012-01-01

    Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, a review of developments and applications of the multi-scale modeling system will be presented. In particular, the microphysics development and its performance for the multi-scale modeling system will be presented.

  11. Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models.

    PubMed

    Kirschner, Denise E; Hunt, C Anthony; Marino, Simeone; Fallahi-Sichani, Mohammad; Linderman, Jennifer J

    2014-01-01

    The use of multi-scale mathematical and computational models to study complex biological processes is becoming increasingly productive. Multi-scale models span a range of spatial and/or temporal scales and can encompass multi-compartment (e.g., multi-organ) models. Modeling advances are enabling virtual experiments to explore and answer questions that are problematic to address in the wet-lab. Wet-lab experimental technologies now allow scientists to observe, measure, record, and analyze experiments focusing on different system aspects at a variety of biological scales. We need the technical ability to mirror that same flexibility in virtual experiments using multi-scale models. Here we present a new approach, tuneable resolution, which can begin providing that flexibility. Tuneable resolution involves fine- or coarse-graining existing multi-scale models at the user's discretion, allowing adjustment of the level of resolution specific to a question, an experiment, or a scale of interest. Tuneable resolution expands options for revising and validating mechanistic multi-scale models, can extend the longevity of multi-scale models, and may increase computational efficiency. The tuneable resolution approach can be applied to many model types, including differential equation, agent-based, and hybrid models. We demonstrate our tuneable resolution ideas with examples relevant to infectious disease modeling, illustrating key principles at work.

  12. Multi-Scale Modeling of Magnetospheric Dynamics

    NASA Technical Reports Server (NTRS)

    Kuznetsova, M. M.; Hesse, M.; Toth, G.

    2012-01-01

    Magnetic reconnection is a key element in many phenomena in space plasma, e.g. Coronal mass Ejections, Magnetosphere substorms. One of the major challenges in modeling the dynamics of large-scale systems involving magnetic reconnection is to quantifY the interaction between global evolution of the magnetosphere and microphysical kinetic processes in diffusion regions near reconnection sites. Recent advances in small-scale kinetic modeling of magnetic reconnection significantly improved our understanding of physical mechanisms controlling the dissipation in the vicinity of the reconnection site in collisionless plasma. However the progress in studies of small-scale geometries was not very helpful for large scale simulations. Global magnetosphere simulations usually include non-ideal processes in terms of numerical dissipation and/or ad hoc anomalous resistivity. Comparative studies of magnetic reconnection in small scale geometries demonstrated that MHD simulations that included non-ideal processes in terms of a resistive term 11 J did not produce fast reconnection rates observed in kinetic simulations. In collisionless magnetospheric plasma, the primary mechanism controlling the dissipation in the vicinity of the reconnection site is nongyrotropic pressure effects with spatial scales comparable with the particle Larmor radius. We utilize the global MHD code BATSRUS and replace ad hoc parameters such as "critical current density" and "anomalous resistivity" with a physically motivated model of dissipation. The primary mechanism controlling the dissipation in the vicinity of the reconnection site in incorporated into MHD description in terms of non-gyrotropic corrections to the induction equation. We will demonstrate that kinetic nongyrotropic effects can significantly alter the global magnetosphere evolution. Our approach allowed for the first time to model loading/unloading cycle in response to steady southward IMF driving. The role of solar wind parameters and

  13. Multi-scale modeling of chemotactic interactions

    NASA Astrophysics Data System (ADS)

    Grima, Ramon

    Biological complexity emerges from the synthesis of biochemical, chemical and physical phenomena. In recent years there has been an intense effort in modeling various cellular systems of interest to understand how the observed complexity emerges from the underlying mechanisms. Most modeling approaches are based on a population description of the cells: these methods, though usually amenable to calculation, are only valid in the limit of large numbers of interacting cells. Many systems of interest involve the interaction of a relatively small number of cells; even biological systems composed of thousands of cells have spatially extended regions over which the number density of cells is small. For the latter cases, population descriptions are not valid and individual based models become a necessity. Such models, usually cellular automaton models, have been numerically studied in recent years; however, these models are not usually amenable to analytic calculation. The work presented in this thesis seeks to fulfill a gap in modeling approaches to the understanding of biocomplexity by constructing an individual based model on which analysis is possible, through the methods of statistical physics and the theory of stochastic processes. This model will be used to study the differences between individual based and population based models and the range of applicability of the latter. For the sake of comparison of the two, new efficient computational algorithms are devised for the simulation of both types of models. We finally complete our multiscale study of modeling by investigating the robustness of individual based models; this meaning a comparison of the results of different microscopic descriptions modeling the same underlying phenomena.

  14. Multi-scale modelling and dynamics

    NASA Astrophysics Data System (ADS)

    Müller-Plathe, Florian

    Moving from a fine-grained particle model to one of lower resolution leads, with few exceptions, to an acceleration of molecular mobility, higher diffusion coefficient, lower viscosities and more. On top of that, the level of acceleration is often different for different dynamical processes as well as for different state points. While the reasons are often understood, the fact that coarse-graining almost necessarily introduces unpredictable acceleration of the molecular dynamics severely limits its usefulness as a predictive tool. There are several attempts under way to remedy these shortcoming of coarse-grained models. On the one hand, we follow bottom-up approaches. They attempt already when the coarse-graining scheme is conceived to estimate their impact on the dynamics. This is done by excess-entropy scaling. On the other hand, we also pursue a top-down development. Here we start with a very coarse-grained model (dissipative particle dynamics) which in its native form produces qualitatively wrong polymer dynamics, as its molecules cannot entangle. This model is modified by additional temporary bonds, so-called slip springs, to repair this defect. As a result, polymer melts and solutions described by the slip-spring DPD model show correct dynamical behaviour. Read more: ``Excess entropy scaling for the segmental and global dynamics of polyethylene melts'', E. Voyiatzis, F. Müller-Plathe, and M.C. Böhm, Phys. Chem. Chem. Phys. 16, 24301-24311 (2014). [DOI: 10.1039/C4CP03559C] ``Recovering the Reptation Dynamics of Polymer Melts in Dissipative Particle Dynamics Simulations via Slip-Springs'', M. Langeloth, Y. Masubuchi, M. C. Böhm, and F. Müller-Plathe, J. Chem. Phys. 138, 104907 (2013). [DOI: 10.1063/1.4794156].

  15. Multi-Scale Modeling of Magnetospheric Reconnection

    NASA Technical Reports Server (NTRS)

    Kuznetsova, M. M.; Hesse, M.; Rastatter, L.; Toth, G.; Dezeeuw, D.; Gomobosi, T.

    2007-01-01

    One of the major challenges in modeling the magnetospheric magnetic reconnection is to quantify the interaction between large-scale global magnetospheric dynamics and microphysical processes in diffusion regions near reconnection sites. There is still considerable debate as to what degree microphysical processes on kinetic scales affect the global evolution and how important it is to substitute numerical dissipation and/or ad hoc anomalous resistivity by a physically motivated model of dissipation. Comparative studies of magnetic reconnection in small scale geometries demonstrated that MHD simulations that included non-ideal processes in terms of a resistive term $\\eta J$ did not produce the fast reconnection rates observed in kinetic simulations. For a broad range of physical parameters in collisionless magnetospheric plasma, the primary mechanism controlling the dissipation in the vicinity of the reconnection site is non-gyrotropic effects with spatial scales comparable with the particle Larmor radius. We utilize the global MHD code BATSRUS and incorporate nongyrotropic effects in diffusion regions in terms of corrections to the induction equation. We developed an algorithm to search for magnetotail reconnection sites, specifically where the magnetic field components perpendicular to the local current direction approaches zero and form an X-type configuration. Spatial scales of the diffusion region and magnitude of the reconnection electric field are calculated selfconsistently using MHD plasma and field parameters in the vicinity of the reconnection site. The location of the reconnection sites is updated during the simulations. To clarify the role of nongyrotropic effects in diffusion region on the global magnetospheric dynamic we perform simulations with steady southward IMF driving of the magnetosphere. Ideal MHD simulations with magnetic reconnection supported by numerical resistivity produce steady configuration with almost stationary near-earth neutral

  16. Multi-Scale Modeling of Plasma Thrusters

    NASA Astrophysics Data System (ADS)

    Batishchev, Oleg

    2004-11-01

    Plasma thrusters are characterized with multiple spatial and temporal scales, which are due to the intrinsic physical processes such as gas ionization, wall effects and plasma acceleration. Characteristic times for hot plasma and cold gas are differing by 6-7 orders of magnitude. The typical collisional mean-free-paths vary by 3-5 orders along the devices. These make questionable a true self-consistent modeling of the thrusters. The latter is vital to the understanding of complex physics, non-linear dynamics and optimization of the performance. To overcome this problem we propose the following approach. All processes are divided into two groups: fast and slow. The slow ones include gas evolution with known sources and ionization sink. The ionization rate, transport coefficients, energy sources are defined during "fast step". Both processes are linked through external iterations. Multiple spatial scales are handled using moving adaptive mesh. Development and application of this method to the VASIMR helicon plasma source and other thrusters will be discussed. Supported by NASA.

  17. Blood Flow: Multi-scale Modeling and Visualization (July 2011)

    SciTech Connect

    2011-01-01

    Multi-scale modeling of arterial blood flow can shed light on the interaction between events happening at micro- and meso-scales (i.e., adhesion of red blood cells to the arterial wall, clot formation) and at macro-scales (i.e., change in flow patterns due to the clot). Coupled numerical simulations of such multi-scale flow require state-of-the-art computers and algorithms, along with techniques for multi-scale visualizations. This animation presents early results of two studies used in the development of a multi-scale visualization methodology. The fisrt illustrates a flow of healthy (red) and diseased (blue) blood cells with a Dissipative Particle Dynamics (DPD) method. Each blood cell is represented by a mesh, small spheres show a sub-set of particles representing the blood plasma, while instantaneous streamlines and slices represent the ensemble average velocity. In the second we investigate the process of thrombus (blood clot) formation, which may be responsible for the rupture of aneurysms, by concentrating on the platelet blood cells, observing as they aggregate on the wall of an aneruysm. Simulation was performed on Kraken at the National Institute for Computational Sciences. Visualization was produced using resources of the Argonne Leadership Computing Facility at Argonne National Laboratory.

  18. Towards Personalized Cardiology: Multi-Scale Modeling of the Failing Heart

    PubMed Central

    Amr, Ali; Neumann, Dominik; Georgescu, Bogdan; Seegerer, Philipp; Kamen, Ali; Haas, Jan; Frese, Karen S.; Irawati, Maria; Wirsz, Emil; King, Vanessa; Buss, Sebastian; Mereles, Derliz; Zitron, Edgar; Keller, Andreas; Katus, Hugo A.; Comaniciu, Dorin; Meder, Benjamin

    2015-01-01

    Background Despite modern pharmacotherapy and advanced implantable cardiac devices, overall prognosis and quality of life of HF patients remain poor. This is in part due to insufficient patient stratification and lack of individualized therapy planning, resulting in less effective treatments and a significant number of non-responders. Methods and Results State-of-the-art clinical phenotyping was acquired, including magnetic resonance imaging (MRI) and biomarker assessment. An individualized, multi-scale model of heart function covering cardiac anatomy, electrophysiology, biomechanics and hemodynamics was estimated using a robust framework. The model was computed on n=46 HF patients, showing for the first time that advanced multi-scale models can be fitted consistently on large cohorts. Novel multi-scale parameters derived from the model of all cases were analyzed and compared against clinical parameters, cardiac imaging, lab tests and survival scores to evaluate the explicative power of the model and its potential for better patient stratification. Model validation was pursued by comparing clinical parameters that were not used in the fitting process against model parameters. Conclusion This paper illustrates how advanced multi-scale models can complement cardiovascular imaging and how they could be applied in patient care. Based on obtained results, it becomes conceivable that, after thorough validation, such heart failure models could be applied for patient management and therapy planning in the future, as we illustrate in one patient of our cohort who received CRT-D implantation. PMID:26230546

  19. Blood Flow: Multi-scale Modeling and Visualization

    SciTech Connect

    2010-01-01

    Multi-scale modeling of arterial blood flow can shed light on the interaction between events happening at micro- and meso-scales (i.e., adhesion of red blood cells to the arterial wall, clot formation) and at macro-scales (i.e., change in flow patterns due to the clot). Coupled numerical simulations of such multi-scale flow require state-of-the-art computers and algorithms. Along with developing methods for multi-scale computations, techniques for multi-scale visualizations must be designed. This animation presents early results of joint efforts of teams from Brown University and Argonne National Laboratory to develop a multi-scale visualization methodology. It illustrates a flow of healthy (red) and diseased (blue) blood cells with a Dissipative Particle Dynamics (DPD) method. Each blood cell is represented by a mesh made of 500 DPD-particles, and small spheres show a sub-set of the DPD particles representing the blood plasma, while instantaneous streamlines and slices represent the ensemble average velocity. Credits: Science: Leopold Grinberg and George Karniadakis, Brown University Visualization: Joseph A. Insley and Michael E. Papka, Argonne National Laboratory This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357. This research was supported in part by the National Science Foundation through the PetaApps program and used TeraGrid resources provided by National Institute for Computational Sciences.

  20. Moist multi-scale models for the hurricane embryo

    SciTech Connect

    Majda, Andrew J.; Xing, Yulong; Mohammadian, Majid

    2010-01-01

    Determining the finite-amplitude preconditioned states in the hurricane embryo, which lead to tropical cyclogenesis, is a central issue in contemporary meteorology. In the embryo there is competition between different preconditioning mechanisms involving hydrodynamics and moist thermodynamics, which can lead to cyclogenesis. Here systematic asymptotic methods from applied mathematics are utilized to develop new simplified moist multi-scale models starting from the moist anelastic equations. Three interesting multi-scale models emerge in the analysis. The balanced mesoscale vortex (BMV) dynamics and the microscale balanced hot tower (BHT) dynamics involve simplified balanced equations without gravity waves for vertical vorticity amplification due to moist heat sources and incorporate nonlinear advective fluxes across scales. The BMV model is the central one for tropical cyclogenesis in the embryo. The moist mesoscale wave (MMW) dynamics involves simplified equations for mesoscale moisture fluctuations, as well as linear hydrostatic waves driven by heat sources from moisture and eddy flux divergences. A simplified cloud physics model for deep convection is introduced here and used to study moist axisymmetric plumes in the BHT model. A simple application in periodic geometry involving the effects of mesoscale vertical shear and moist microscale hot towers on vortex amplification is developed here to illustrate features of the coupled multi-scale models. These results illustrate the use of these models in isolating key mechanisms in the embryo in a simplified content.

  1. Science based integrated approach to advanced nuclear fuel development - integrated multi-scale multi-physics hierarchical modeling and simulation framework Part III: cladding

    SciTech Connect

    Tome, Carlos N; Caro, J A; Lebensohn, R A; Unal, Cetin; Arsenlis, A; Marian, J; Pasamehmetoglu, K

    2010-01-01

    Advancing the performance of Light Water Reactors, Advanced Nuclear Fuel Cycles, and Advanced Reactors, such as the Next Generation Nuclear Power Plants, requires enhancing our fundamental understanding of fuel and materials behavior under irradiation. The capability to accurately model the nuclear fuel systems to develop predictive tools is critical. Not only are fabrication and performance models needed to understand specific aspects of the nuclear fuel, fully coupled fuel simulation codes are required to achieve licensing of specific nuclear fuel designs for operation. The backbone of these codes, models, and simulations is a fundamental understanding and predictive capability for simulating the phase and microstructural behavior of the nuclear fuel system materials and matrices. In this paper we review the current status of the advanced modeling and simulation of nuclear reactor cladding, with emphasis on what is available and what is to be developed in each scale of the project, how we propose to pass information from one scale to the next, and what experimental information is required for benchmarking and advancing the modeling at each scale level.

  2. Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models

    PubMed Central

    Kirschner, Denise E; Hunt, C Anthony; Marino, Simeone; Fallahi-Sichani, Mohammad; Linderman, Jennifer J

    2014-01-01

    The use of multi-scale mathematical and computational models to study complex biological processes is becoming increasingly productive. Multi-scale models span a range of spatial and/or temporal scales and can encompass multi-compartment (e.g., multi-organ) models. Modeling advances are enabling virtual experiments to explore and answer questions that are problematic to address in the wet-lab. Wet-lab experimental technologies now allow scientists to observe, measure, record, and analyze experiments focusing on different system aspects at a variety of biological scales. We need the technical ability to mirror that same flexibility in virtual experiments using multi-scale models. Here we present a new approach, tuneable resolution, which can begin providing that flexibility. Tuneable resolution involves fine- or coarse-graining existing multi-scale models at the user's discretion, allowing adjustment of the level of resolution specific to a question, an experiment, or a scale of interest. Tuneable resolution expands options for revising and validating mechanistic multi-scale models, can extend the longevity of multi-scale models, and may increase computational efficiency. The tuneable resolution approach can be applied to many model types, including differential equation, agent-based, and hybrid models. We demonstrate our tuneable resolution ideas with examples relevant to infectious disease modeling, illustrating key principles at work. WIREs Syst Biol Med 2014, 6:225–245. doi:10.1002/wsbm.1270 How to cite this article: WIREs Syst Biol Med 2014, 6:289–309. doi:10.1002/wsbm.1270 PMID:24810243

  3. A Goddard Multi-Scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, W.K.; Anderson, D.; Atlas, R.; Chern, J.; Houser, P.; Hou, A.; Lang, S.; Lau, W.; Peters-Lidard, C.; Kakar, R.; Kumar, S.; Lapenta, W.; Li, X.; Matsui, T.; Rienecker, M.; Shen, B.W.; Shi, J.J.; Simpson, J.; Zeng, X.

    2008-01-01

    Numerical cloud resolving models (CRMs), which are based the non-hydrostatic equations of motion, have been extensively applied to cloud-scale and mesoscale processes during the past four decades. Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that CRMs agree with observations in simulating various types of clouds and cloud systems from different geographic locations. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that Numerical Weather Prediction (NWP) and regional scale model can be run in grid size similar to cloud resolving model through nesting technique. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a szrper-parameterization or multi-scale modeling -framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameterization. NASA satellite and field campaign can provide initial conditions as well as validation through utilizing the Earth Satellite simulators. At Goddard, we have developed a multi-scale modeling system with unified physics. The modeling system consists a coupled GCM-CRM (or MMF); a state-of-the-art weather research forecast model (WRF) and a cloud-resolving model (Goddard Cumulus Ensemble model). In these models, the same microphysical schemes (2ICE, several 3ICE), radiation (including explicitly calculated cloud optical properties), and surface models are applied. In addition, a comprehensive unified Earth Satellite

  4. Multi-scale modelling of elastic moduli of trabecular bone

    PubMed Central

    Hamed, Elham; Jasiuk, Iwona; Yoo, Andrew; Lee, YikHan; Liszka, Tadeusz

    2012-01-01

    We model trabecular bone as a nanocomposite material with hierarchical structure and predict its elastic properties at different structural scales. The analysis involves a bottom-up multi-scale approach, starting with nanoscale (mineralized collagen fibril) and moving up the scales to sub-microscale (single lamella), microscale (single trabecula) and mesoscale (trabecular bone) levels. Continuum micromechanics methods, composite materials laminate theory and finite-element methods are used in the analysis. Good agreement is found between theoretical and experimental results. PMID:22279160

  5. A Goddard Multi-Scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2008-01-01

    A multi-scale modeling system with unified physics has been developed at NASA Goddard Space Flight Center (GSFC). The system consists of an MMF, the coupled NASA Goddard finite-volume GCM (fvGCM) and Goddard Cumulus Ensemble model (GCE, a CRM); the state-of-the-art Weather Research and Forecasting model (WRF) and the stand alone GCE. These models can share the same microphysical schemes, radiation (including explicitly calculated cloud optical properties), and surface models that have been developed, improved and tested for different environments. The following is presented in this report: (1) a brief review of the GCE model and its applications on the impact of aerosols on deep precipitation processes, (2) the Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) a discussion on the Goddard WRF version (its developments and applications).

  6. A Novel Spectral Approach to Multi-Scale Modeling

    NASA Astrophysics Data System (ADS)

    Landi, Giacomo

    2011-12-01

    In this work, we present a novel approach for predicting the elastic, thermo-elastic and plastic fields in three-dimensional (3-D) voxel-based microstructure datasets subjected to uniform periodic boundary conditions. Such localization relationships (linkages) lie at the core of all multi-scale modeling frameworks and can be efficiently formulated in a Discrete Fourier Transforms (DFT) -based knowledge system. This new formalism has its theoretical roots in the statistical continuum theories developed originally by Kroner [1]. However, in the approach described by Kroner, the terms in the series were established by selecting a reference medium and numerically evaluating a complex series of nested convolution integrals. This approach is largely hampered by the principal value problem, and exhibits high sensitivity to the properties of the selected reference medium. In the present work, the same series expressions have been recast into much more computationally efficient representations using DFTs. The spectral analysis transforms the complex integral relations into relatively simple algebraic expressions involving polynomials of structure parameters and morphology-independent influence coefficients. These coefficients need to be established only once for a given material system. The main advantage of the new DFT-based framework is that it allows easy calibration of Kroner's expansions to results from finite element methods, thereby overcoming all of the main obstacles associated with the principal value problem and the need to select a reference medium. This approach can be seen as an efficient procedure for data-mining the results from computationally expensive numerical models and establishing the underlying knowledge systems at a selected length scale in multi-scale modeling problems. The set of influence coefficients described above constitutes the underlying knowledge for a given deformation and can be easily stored and recalled as and when needed in a multi-scale

  7. Multi-Scale Modeling of Hypersonic Gas Flow

    NASA Astrophysics Data System (ADS)

    Boyd, Iain D.

    On March 27, 2004, NASA successfully flew the X-43A hypersonic test flight vehicle at a velocity of 5000 mph to break the aeronautics speed record that had stood for over 35 years. The final flight of the X-43A on November 16, 2004 further increased the speed record to 6,600 mph which is almost ten times the speed of sound. The very high speed attainable by hypersonic airplanes could revolutionize air travel by dramatically reducing inter-continental flight times. For example, a hypersonic flight from New York to Sydney, Australia, a distance of 10,000 miles, would take less than 2 h. Reusable hypersonic vehicles are also being researched to significantly reduce the cost of access to space. Computer modeling of the gas flows around hypersonic vehicles will play a critical part in their development. This article discusses the conditions that can prevail in certain hypersonic gas flows that require a multi-scale modeling approach.

  8. Multi-Scale Coupling in Ocean and Climate Modeling

    SciTech Connect

    Zhengyu Liu, Leslie Smith

    2009-08-14

    We have made significant progress on several projects aimed at understanding multi-scale dynamics in geophysical flows. Large-scale flows in the atmosphere and ocean are influenced by stable density stratification and rotation. The presence of stratification and rotation has important consequences through (i) the conservation of potential vorticity q = {omega} {center_dot} {del} {rho}, where {omega} is the total vorticity and {rho} is the density, and (ii) the existence of waves that affect the redistribution of energy from a given disturbance to the flow. Our research is centered on quantifying the effects of potential vorticity conservation and of wave interactions for the coupling of disparate time and space scales in the oceans and the atmosphere. Ultimately we expect the work to help improve predictive capabilities of atmosphere, ocean and climate modelers. The main findings of our research projects are described.

  9. A Goddard Multi-Scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2010-01-01

    A multi-scale modeling system with unified physics has been developed at NASA Goddard Space Flight Center (GSFC). The system consists of an MMF, the coupled NASA Goddard finite-volume GCM (fvGCM) and Goddard Cumulus Ensemble model (GCE, a CRM); the state-of-the-art Weather Research and Forecasting model (WRF) and the stand alone GCE. These models can share the same microphysical schemes, radiation (including explicitly calculated cloud optical properties), and surface models that have been developed, improved and tested for different environments. In this talk, I will present: (1) A brief review on GCE model and its applications on the impact of the aerosol on deep precipitation processes, (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) A discussion on the Goddard WRF version (its developments and applications). We are also performing the inline tracer calculation to comprehend the physical processes (i.e., boundary layer and each quadrant in the boundary layer) related to the development and structure of hurricanes and mesoscale convective systems. In addition, high - resolution (spatial. 2km, and temporal, I minute) visualization showing the model results will be presented.

  10. Multi-scale modeling of the CD8 immune response

    NASA Astrophysics Data System (ADS)

    Barbarroux, Loic; Michel, Philippe; Adimy, Mostafa; Crauste, Fabien

    2016-06-01

    During the primary CD8 T-Cell immune response to an intracellular pathogen, CD8 T-Cells undergo exponential proliferation and continuous differentiation, acquiring cytotoxic capabilities to address the infection and memorize the corresponding antigen. After cleaning the organism, the only CD8 T-Cells left are antigen-specific memory cells whose role is to respond stronger and faster in case they are presented this very same antigen again. That is how vaccines work: a small quantity of a weakened pathogen is introduced in the organism to trigger the primary response, generating corresponding memory cells in the process, giving the organism a way to defend himself in case it encounters the same pathogen again. To investigate this process, we propose a non linear, multi-scale mathematical model of the CD8 T-Cells immune response due to vaccination using a maturity structured partial differential equation. At the intracellular scale, the level of expression of key proteins is modeled by a delay differential equation system, which gives the speeds of maturation for each cell. The population of cells is modeled by a maturity structured equation whose speeds are given by the intracellular model. We focus here on building the model, as well as its asymptotic study. Finally, we display numerical simulations showing the model can reproduce the biological dynamics of the cell population for both the primary response and the secondary responses.

  11. A Goddard Multi-Scale Modeling System with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2010-01-01

    A multi-scale modeling system with unified physics has been developed at NASA Goddard Space Flight Center (GSFC). The system consists of an MMF, the coupled NASA Goddard finite-volume GCM (fvGCM) and Goddard Cumulus Ensemble model (GCE, a CRM); the state-of-the-art Weather Research and Forecasting model (WRF) and the stand alone GCE. These models can share the same microphysical schemes, radiation (including explicitly calculated cloud optical properties), and surface models that have been developed, improved and tested for different environments. In this talk, I will present: (1) A brief review on GCE model and its applications on the impact of the aerosol on deep precipitation processes, (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) A discussion on the Goddard WRF version (its developments and applications). We are also performing the inline tracer calculation to comprehend the ph ysical processes (i.e., boundary layer and each quadrant in the boundary layer) related to the development and structure of hurricanes and mesoscale convective systems.

  12. Extreme Precipitation in a Multi-Scale Modeling Framework

    NASA Astrophysics Data System (ADS)

    Phillips, M.; Denning, S.; Arabi, M.

    2015-12-01

    Extreme precipitation events are characterized by infrequent but large magnitude accummulatations that generally occur on scales belowthat resolved by the typical Global Climate Model. The Multi-scale Modeling Framework allows for information about the precipitation on these scales to be simulated for long periods of time without the large computational resources required for the use of a full cloud permitting model. The Community Earth System Model was run for 30 years in both its MMF and GCM modes, and the annual maximum series of 24 hour precipitation accumulations were used to estimate the parameters of statistical distributions. The distributions generated from model ouput were then fit to a General Extreme Value distribution and evaluated against observations. These results indicate that the MMF produces extreme precipitation with a statistical distribution that closely resembles that of observations and motivates the continued use of the MMF for analysis of extreme precipitation, and shows an improvement over the traditional GCM. The improvement in statistical distributions of annual maxima is greatest in regions that are dominated by convective precipitation where the small-scale information provided by the MMF heavily influences precipitation processes.

  13. Multi-Scale Modeling of Cross-Linked Nanotube Materials

    NASA Technical Reports Server (NTRS)

    Frankland, S. J. V.; Odegard, G. M.; Herzog, M. N.; Gates, T. S.; Fay, C. C.

    2005-01-01

    The effect of cross-linking single-walled carbon nanotubes on the Young's modulus of a nanotube-reinforced composite is modeled with a multi-scale method. The Young's modulus is predicted as a function of nanotube volume fraction and cross-link density. In this method, the constitutive properties of molecular representative volume elements are determined using molecular dynamics simulation and equivalent-continuum modeling. The Young's modulus is subsequently calculated for cross-linked nanotubes in a matrix which consists of the unreacted cross-linking agent. Two different cross-linking agents are used in this study, one that is short and rigid (Molecule A), and one that is long and flexible (Molecule B). Direct comparisons between the predicted elastic constants are made for the models in which the nanotubes are either covalently bonded or not chemically bonded to the cross-linking agent. At a nanotube volume fraction of 10%, the Young's modulus of Material A is not affected by nanotube crosslinking, while the Young's modulus of Material B is reduced by 64% when the nanotubes are cross-linked relative to the non-cross-linked material with the same matrix.

  14. Multi-scale Modeling of Plasticity in Tantalum.

    SciTech Connect

    Lim, Hojun; Battaile, Corbett Chandler.; Carroll, Jay; Buchheit, Thomas E.; Boyce, Brad; Weinberger, Christopher

    2015-12-01

    In this report, we present a multi-scale computational model to simulate plastic deformation of tantalum and validating experiments. In atomistic/ dislocation level, dislocation kink- pair theory is used to formulate temperature and strain rate dependent constitutive equations. The kink-pair theory is calibrated to available data from single crystal experiments to produce accurate and convenient constitutive laws. The model is then implemented into a BCC crystal plasticity finite element method (CP-FEM) model to predict temperature and strain rate dependent yield stresses of single and polycrystalline tantalum and compared with existing experimental data from the literature. Furthermore, classical continuum constitutive models describing temperature and strain rate dependent flow behaviors are fit to the yield stresses obtained from the CP-FEM polycrystal predictions. The model is then used to conduct hydro- dynamic simulations of Taylor cylinder impact test and compared with experiments. In order to validate the proposed tantalum CP-FEM model with experiments, we introduce a method for quantitative comparison of CP-FEM models with various experimental techniques. To mitigate the effects of unknown subsurface microstructure, tantalum tensile specimens with a pseudo-two-dimensional grain structure and grain sizes on the order of millimeters are used. A technique combining an electron back scatter diffraction (EBSD) and high resolution digital image correlation (HR-DIC) is used to measure the texture and sub-grain strain fields upon uniaxial tensile loading at various applied strains. Deformed specimens are also analyzed with optical profilometry measurements to obtain out-of- plane strain fields. These high resolution measurements are directly compared with large-scale CP-FEM predictions. This computational method directly links fundamental dislocation physics to plastic deformations in the grain-scale and to the engineering-scale applications. Furthermore, direct

  15. Modeling of Multi-Scale Channeling Phenomena in Porous Flow

    NASA Astrophysics Data System (ADS)

    Räss, Ludovic; Omlin, Samuel; Yarushina, Viktoriya; Simon, Nina; Podladchikov, Yuri

    2015-04-01

    Predictive modeling of fluid percolation through tight porous rocks is critical to evaluate environmental risks associated with waste storage and reservoir operations. To understand the evolution of two-phase mixtures of fluid and solid it is insufficient to only combine single-phase fluid flow methods and solid mechanics. A proper coupling of these two different multi-scales physical processes is required to describe the complex evolution of permeability and porosity in space and in time. We conduct numerical modeling experiments in geometrically simple but physically complex systems of stressed rocks containing self-focusing porous flow. Our model is physically and thermodynamically consistent and describes the formation and evolution of fluid pathways. The model consists of a system of coupled equations describing poro-elasto-viscous deformation and flow. Nonlinearity of the solid rheology is also taken into account. We have developed a numerical application based on an iterative finite difference scheme that runs on mutli-GPUs cluster in parallel. In order to validate these models, we consider the largest CO2 sequestration project in operation at the Sleipner field in the Norwegian North Sea. Attempts to match the observations at Sleipner using conventional reservoir simulations fail to capture first order observations, such as the seemingly effortless vertical flow of CO2 through low permeability shale layers and the formation of focused flow channels or chimneys. Conducted high-resolution three-dimensional numerical simulations predict the formation of dynamically evolving high porosity and permeability pathways as a natural outcome of porous flow nonlinearly coupled with rock deformation, which may trigger leakage through low permeability barriers.

  16. Quasi-3D Algorithm in Multi-scale Modeling Framework

    NASA Astrophysics Data System (ADS)

    Jung, J.; Arakawa, A.

    2008-12-01

    As discussed in the companion paper by Arakawa and Jung, the Quasi-3D (Q3D) Multi-scale Modeling Framework (MMF) is a 4D estimation/prediction framework that combines a GCM with a 3D anelastic vector vorticity equation model (VVM) applied to a Q3D network of horizontal grid points. This paper presents an outline of the recently revised Q3D algorithm and a highlight of the results obtained by application of the algorithm to an idealized model setting. The Q3D network of grid points consists of two sets of grid-point arrays perpendicular to each other. For a scalar variable, for example, each set consists of three parallel rows of grid points. Principal and supplementary predictions are made on the central and the two adjacent rows, respectively. The supplementary prediction is to allow the principal prediction be three-dimensional at least to the second-order accuracy. To accommodate a higher-order accuracy and to make the supplementary predictions formally three-dimensional, a few rows of ghost points are added at each side of the array. Values at these ghost points are diagnostically determined by a combination of statistical estimation and extrapolation. The basic structure of the estimation algorithm is determined in view of the global stability of Q3D advection. The algorithm is calibrated using the statistics of past data at and near the intersections of the two sets of grid- point arrays. Since the CRM in the Q3D MMF extends beyond individual GCM boxes, the CRM can be a GCM by itself. However, it is better to couple the CRM with the GCM because (1) the CRM is a Q3D CRM based on a highly anisotropic network of grid points and (2) coupling with a GCM makes it more straightforward to inherit our experience with the conventional GCMs. In the coupled system we have selected, prediction of thermdynamic variables is almost entirely done by the Q3D CRM with no direct forcing by the GCM. The coupling of the dynamics between the two components is through mutual

  17. PECASE - Multi-Scale Experiments and Modeling in Wall Turbulence

    DTIC Science & Technology

    2014-12-23

    characterizing the three-dimensional spectrum of the streamwise velocity fluctuations using time-resolved particle image velocimetry at a range of...spectrum of the streamwise velocity fluctuations using time-resolved particle image velocimetry at a range of wall-normal locations, and extending a two...in canonical and non-canonical turbulent boundary layers using fast Particle Image Velocimetry in order to identify the influence of multi-scale

  18. Quasi-3D Multi-scale Modeling Framework Development

    NASA Astrophysics Data System (ADS)

    Arakawa, A.; Jung, J.

    2008-12-01

    When models are truncated in or near an energetically active range of the spectrum, model physics must be changed as the resolution changes. The model physics of GCMs and that of CRMs are, however, quite different from each other and at present there is no unified formulation of model physics that automatically provides transition between these model physics. The Quasi-3D (Q3D) Multi-scale Modeling Framework (MMF) is an attempt to bridge this gap. Like the recently proposed Heterogeneous Multiscale Method (HMM) (E and Engquist 2003), MMF combines a macroscopic model, GCM, and a microscopic model, CRM. Unlike the traditional multiscale methods such as the multi-grid and adapted mesh refinement techniques, HMM and MMF are for solving multi-physics problems. They share the common objective "to design combined macroscopic-microscopic computational methods that are much more efficient than solving the full microscopic model and at the same time give the information we need" (E et al. 2008). The question is then how to meet this objective in practice, which can be highly problem dependent. In HHM, the efficiency is gained typically by localization of the microscale problem. Following the pioneering work by Grabowski and Smolarkiewicz (1999) and Grabowski (2001), MMF takes advantage of the fact that 2D CRMs are reasonably successful in simulating deep clouds. In this approach, the efficiency is gained by sacrificing the three-dimensionality of cloud-scale motion. It also "localizes" the algorithm through embedding a CRM in each GCM grid box using cyclic boundary condition. The Q3D MMF is an attempt to reduce the expense due to these constraints by partially including the cloud-scale 3D effects and extending the CRM beyond individual GCM grid boxes. As currently formulated, the Q3D MMF is a 4D estimation/prediction framework that combines a GCM with a 3D anelastic cloud-resolving vector vorticity equation model (VVM) applied to a network of horizontal grids. The network

  19. A Multi-Scale Modeling of Laser Cladding Process (Preprint)

    DTIC Science & Technology

    2006-04-01

    possibilities to alter a component at its surface. Despite immense potentials and advancements, the process model of microstructure evolution and its coupling...with macro parameter of laser cladding process has not been fully developed. To address this issue, a process model of microstructure evolution has

  20. Training Systems Modelers through the Development of a Multi-scale Chagas Disease Risk Model

    NASA Astrophysics Data System (ADS)

    Hanley, J.; Stevens-Goodnight, S.; Kulkarni, S.; Bustamante, D.; Fytilis, N.; Goff, P.; Monroy, C.; Morrissey, L. A.; Orantes, L.; Stevens, L.; Dorn, P.; Lucero, D.; Rios, J.; Rizzo, D. M.

    2012-12-01

    The goal of our NSF-sponsored Division of Behavioral and Cognitive Sciences grant is to create a multidisciplinary approach to develop spatially explicit models of vector-borne disease risk using Chagas disease as our model. Chagas disease is a parasitic disease endemic to Latin America that afflicts an estimated 10 million people. The causative agent (Trypanosoma cruzi) is most commonly transmitted to humans by blood feeding triatomine insect vectors. Our objectives are: (1) advance knowledge on the multiple interacting factors affecting the transmission of Chagas disease, and (2) provide next generation genomic and spatial analysis tools applicable to the study of other vector-borne diseases worldwide. This funding is a collaborative effort between the RSENR (UVM), the School of Engineering (UVM), the Department of Biology (UVM), the Department of Biological Sciences (Loyola (New Orleans)) and the Laboratory of Applied Entomology and Parasitology (Universidad de San Carlos). Throughout this five-year study, multi-educational groups (i.e., high school, undergraduate, graduate, and postdoctoral) will be trained in systems modeling. This systems approach challenges students to incorporate environmental, social, and economic as well as technical aspects and enables modelers to simulate and visualize topics that would either be too expensive, complex or difficult to study directly (Yasar and Landau 2003). We launch this research by developing a set of multi-scale, epidemiological models of Chagas disease risk using STELLA® software v.9.1.3 (isee systems, inc., Lebanon, NH). We use this particular system dynamics software as a starting point because of its simple graphical user interface (e.g., behavior-over-time graphs, stock/flow diagrams, and causal loops). To date, high school and undergraduate students have created a set of multi-scale (i.e., homestead, village, and regional) disease models. Modeling the system at multiple spatial scales forces recognition that

  1. Multi-scale modelling of uranyl chloride solutions

    SciTech Connect

    Nguyen, Thanh-Nghi; Duvail, Magali Villard, Arnaud; Dufrêche, Jean-François; Molina, John Jairo; Guilbaud, Philippe

    2015-01-14

    Classical molecular dynamics simulations with explicit polarization have been successfully used to determine the structural and thermodynamic properties of binary aqueous solutions of uranyl chloride (UO{sub 2}Cl{sub 2}). Concentrated aqueous solutions of uranyl chloride have been studied to determine the hydration properties and the ion-ion interactions. The bond distances and the coordination number of the hydrated uranyl are in good agreement with available experimental data. Two stable positions of chloride in the second hydration shell of uranyl have been identified. The UO{sub 2}{sup 2+}-Cl{sup −} association constants have also been calculated using a multi-scale approach. First, the ion-ion potential averaged over the solvent configurations at infinite dilution (McMillan-Mayer potential) was calculated to establish the dissociation/association processes of UO{sub 2}{sup 2+}-Cl{sup −} ion pairs in aqueous solution. Then, the association constant was calculated from this potential. The value we obtained for the association constant is in good agreement with the experimental result (K{sub UO{sub 2Cl{sup +}}} = 1.48 l mol{sup −1}), but the resulting activity coefficient appears to be too low at molar concentration.

  2. Transferring Multi-Scale Approaches from 3d City Modeling to Ifc-Based Tunnel Modeling

    NASA Astrophysics Data System (ADS)

    Borrmann, A.; Kolbe, T. H.; Donaubauer, A.; Steuer, H.; Jubierre, J. R.

    2013-09-01

    A multi-scale representation of the built environment is required to provide information with the adequate level of detail (LoD) for different use cases and objectives. This applies not only to the visualization of city and building models, but in particular to their use in the context of planning and analysis tasks. While in the field of Geographic Information Systems, the handling of multi-scale representations is well established and understood, no formal approaches for incorporating multi-scale methods exist in the field of Building Information Modeling (BIM) so far. However, these concepts are much needed to better support highly dynamic planning processes that make use of very rough information about the facility under design in the early stages and provide increasingly detailed and fine-grained information in later stages. To meet these demands, this paper presents a comprehensive concept for incorporating multi-scale representations with infrastructural building information models, with a particular focus on the representation of shield tunnels. Based on a detailed analysis of the data modeling methods used in CityGML for capturing multiscale representations and the requirements present in the context of infrastructure planning projects, we discuss potential extensions to the BIM data model Industry Foundation Classes (IFC). Particular emphasis is put on providing means for preserving the consistency of the representation across the different Levels-of-Detail (LoD). To this end we make use of a procedural geometry description which makes it possible to define explicit dependencies between geometric entities on different LoDs. The modification of an object on a coarse level consequently results in an automated update of all dependent objects on the finer levels. Finally we discuss the transformation of the IFC-based multi-scale tunnel model into a CityGML compliant tunnel representation.

  3. Probabilistic multi-scale modeling of pathogen dynamics in rivers

    NASA Astrophysics Data System (ADS)

    Packman, A. I.; Drummond, J. D.; Aubeneau, A. F.

    2014-12-01

    Most parameterizations of microbial dynamics and pathogen transport in surface waters rely on classic assumptions of advection-diffusion behavior in the water column and limited interactions between the water column and sediments. However, recent studies have shown that strong surface-subsurface interactions produce a wide range of transport timescales in rivers, and greatly the opportunity for long-term retention of pathogens in sediment beds and benthic biofilms. We present a stochastic model for pathogen dynamics, based on continuous-time random walk theory, that properly accounts for such diverse transport timescales, along with the remobilization and inactivation of pathogens in storage reservoirs. By representing pathogen dynamics probabilistically, the model framework enables diverse local-scale processes to be incorporated in system-scale models. We illustrate the application of the model to microbial dynamics in rivers based on the results of a tracer injection experiment. In-stream transport and surface-subsurface interactions are parameterized based on observations of conservative tracer transport, while E. coli retention and inactivation in sediments is parameterized based on direct local-scale experiments. The results indicate that sediments are an important reservoir of enteric organisms in rivers, and slow remobilization from sediments represents a long-term source of bacteria to streams. Current capability, potential advances, and limitations of this model framework for assessing pathogen transmission risks will be discussed. Because the transport model is probabilistic, it is amenable to incorporation into risk models, but a lack of characterization of key microbial processes in sediments and benthic biofilms hinders current application.

  4. Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models.

    PubMed

    Jagiella, Nick; Rickert, Dennis; Theis, Fabian J; Hasenauer, Jan

    2017-02-22

    Mechanistic understanding of multi-scale biological processes, such as cell proliferation in a changing biological tissue, is readily facilitated by computational models. While tools exist to construct and simulate multi-scale models, the statistical inference of the unknown model parameters remains an open problem. Here, we present and benchmark a parallel approximate Bayesian computation sequential Monte Carlo (pABC SMC) algorithm, tailored for high-performance computing clusters. pABC SMC is fully automated and returns reliable parameter estimates and confidence intervals. By running the pABC SMC algorithm for ∼10(6) hr, we parameterize multi-scale models that accurately describe quantitative growth curves and histological data obtained in vivo from individual tumor spheroid growth in media droplets. The models capture the hybrid deterministic-stochastic behaviors of 10(5)-10(6) of cells growing in a 3D dynamically changing nutrient environment. The pABC SMC algorithm reliably converges to a consistent set of parameters. Our study demonstrates a proof of principle for robust, data-driven modeling of multi-scale biological systems and the feasibility of multi-scale model parameterization through statistical inference.

  5. ONE-ATMOSPHERE DYNAMICS DESCRIPTION IN THE MODELS-3 COMMUNITY MULTI-SCALE QUALITY (CMAQ) MODELING SYSTEM

    EPA Science Inventory

    This paper proposes a general procedure to link meteorological data with air quality models, such as U.S. EPA's Models-3 Community Multi-scale Air Quality (CMAQ) modeling system. CMAQ is intended to be used for studying multi-scale (urban and regional) and multi-pollutant (ozon...

  6. Multi-scale modelling of rubber-like materials and soft tissues: an appraisal

    PubMed Central

    Puglisi, G.

    2016-01-01

    We survey, in a partial way, multi-scale approaches for the modelling of rubber-like and soft tissues and compare them with classical macroscopic phenomenological models. Our aim is to show how it is possible to obtain practical mathematical models for the mechanical behaviour of these materials incorporating mesoscopic (network scale) information. Multi-scale approaches are crucial for the theoretical comprehension and prediction of the complex mechanical response of these materials. Moreover, such models are fundamental in the perspective of the design, through manipulation at the micro- and nano-scales, of new polymeric and bioinspired materials with exceptional macroscopic properties. PMID:27118927

  7. SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling.

    PubMed

    Solovyev, Alexey; Mikheev, Maxim; Zhou, Leming; Dutta-Moscato, Joyeeta; Ziraldo, Cordelia; An, Gary; Vodovotz, Yoram; Mi, Qi

    2010-01-01

    Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform for Agent-based Representation of Knowledge), a framework for agent-based modeling specifically designed for systems-level biomedical model development. SPARK is a stand-alone application written in Java. It provides a user-friendly interface, and a simple programming language for developing Agent-Based Models (ABMs). SPARK has the following features specialized for modeling biomedical systems: 1) continuous space that can simulate real physical space; 2) flexible agent size and shape that can represent the relative proportions of various cell types; 3) multiple spaces that can concurrently simulate and visualize multiple scales in biomedical models; 4) a convenient graphical user interface. Existing ABMs of diabetic foot ulcers and acute inflammation were implemented in SPARK. Models of identical complexity were run in both NetLogo and SPARK; the SPARK-based models ran two to three times faster.

  8. Using Multi-Scale Modeling Systems to Study the Precipitation Processes

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2010-01-01

    In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, a review of developments and applications of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the interactions between clouds, precipitation, and aerosols will be presented. Also how to use of the multi-satellite simulator to improve precipitation processes will be discussed.

  9. Using Multi-Scale Modeling Systems and Satellite Data to Study the Precipitation Processes

    NASA Technical Reports Server (NTRS)

    Tao, Wei--Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.

    2010-01-01

    In recent years, exponentially increasing computer power extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 sq km in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale models can be run in grid size similar to cloud resolving models through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model). (2) a regional scale model (a NASA unified weather research and forecast, W8F). (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, a review of developments and applications of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling systems to study the interactions between clouds, precipitation, and aerosols will be presented. Also how to use the multi-satellite simulator to improve precipitation processes will be discussed.

  10. Microphysics in the Multi-Scale Modeling Systems with Unified Physics

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.

    2011-01-01

    In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (l) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, the microphysics developments of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the heavy precipitation processes will be presented.

  11. Multi-scale finite element modeling allows the mechanics of amphibian neurulation to be elucidated

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoguang; Brodland, G. Wayne

    2008-03-01

    The novel multi-scale computational approach introduced here makes possible a new means for testing hypotheses about the forces that drive specific morphogenetic movements. A 3D model based on this approach is used to investigate neurulation in the axolotl (Ambystoma mexicanum), a type of amphibian. The model is based on geometric data from 3D surface reconstructions of live embryos and from serial sections. Tissue properties are described by a system of cell-based constitutive equations, and parameters in the equations are determined from physical tests. The model includes the effects of Shroom-activated neural ridge reshaping and lamellipodium-driven convergent extension. A typical whole-embryo model consists of 10 239 elements and to run its 100 incremental time steps requires 2 days. The model shows that a normal phenotype does not result if lamellipodium forces are uniform across the width of the neural plate; but it can result if the lamellipodium forces decrease from a maximum value at the mid-sagittal plane to zero at the plate edge. Even the seemingly simple motions of neurulation are found to contain important features that would remain hidden, they were not studied using an advanced computational model. The present model operates in a setting where data are extremely sparse and an important outcome of the study is a better understanding of the role of computational models in such environments.

  12. Downscaling modelling system for multi-scale air quality forecasting

    NASA Astrophysics Data System (ADS)

    Nuterman, R.; Baklanov, A.; Mahura, A.; Amstrup, B.; Weismann, J.

    2010-09-01

    Urban modelling for real meteorological situations, in general, considers only a small part of the urban area in a micro-meteorological model, and urban heterogeneities outside a modelling domain affect micro-scale processes. Therefore, it is important to build a chain of models of different scales with nesting of higher resolution models into larger scale lower resolution models. Usually, the up-scaled city- or meso-scale models consider parameterisations of urban effects or statistical descriptions of the urban morphology, whereas the micro-scale (street canyon) models are obstacle-resolved and they consider a detailed geometry of the buildings and the urban canopy. The developed system consists of the meso-, urban- and street-scale models. First, it is the Numerical Weather Prediction (HIgh Resolution Limited Area Model) model combined with Atmospheric Chemistry Transport (the Comprehensive Air quality Model with extensions) model. Several levels of urban parameterisation are considered. They are chosen depending on selected scales and resolutions. For regional scale, the urban parameterisation is based on the roughness and flux corrections approach; for urban scale - building effects parameterisation. Modern methods of computational fluid dynamics allow solving environmental problems connected with atmospheric transport of pollutants within urban canopy in a presence of penetrable (vegetation) and impenetrable (buildings) obstacles. For local- and micro-scales nesting the Micro-scale Model for Urban Environment is applied. This is a comprehensive obstacle-resolved urban wind-flow and dispersion model based on the Reynolds averaged Navier-Stokes approach and several turbulent closures, i.e. k -ɛ linear eddy-viscosity model, k - ɛ non-linear eddy-viscosity model and Reynolds stress model. Boundary and initial conditions for the micro-scale model are used from the up-scaled models with corresponding interpolation conserving the mass. For the boundaries a

  13. Modelling multi-scale deformation of amorphous glassy polymers with experimentally motivated evolution of the microstructure

    NASA Astrophysics Data System (ADS)

    Engqvist, Jonas; Wallin, Mathias; Ristinmaa, Matti; Hall, Stephen A.; Plivelic, Tomás S.

    2016-11-01

    Novel experimental data, obtained recently using advanced multi-scale experiments, have been used to develop a micro-mechanically motivated constitutive model for amorphous glassy polymers. Taking advantage of the experiments, the model makes use of a microstructural deformation gradient to incorporate the experimentally obtained deformation of the microstructure, as well as its evolving orientation. By comparing results from the model to experimental data, it is shown that the proposed approach is able to accurately predict glassy polymer deformation over a wide range of length-scales, from the macroscopic response (mm range) down to the deformation of the microstructure (nm range). The proposed model is evaluated by comparing the numerical response to experimental results on multiple scales from an inhomogeneous cold drawing experiment of glassy polycarbonate. Besides the macroscopic force-displacement response, a qualitative comparison of the deformation field at the surface of the specimen is performed. Furthermore, the predicted evolution of the fabric orientation is compared to experimental results obtained from X-ray scattering experiments. The model shows very good agreement with the experimental data over a wide range of length scales.

  14. Multi-Scale Modeling of Cementitious Materials (Briefing Chart)

    DTIC Science & Technology

    2014-08-31

    FEA approach. Voxels are generated for a heterogeneous cementitious material (Type-I cement ) consisting of typical volume fractions of various...for public release; distribution is unlimited. Micromechanics Based Representative Volume Element Modeling of Heterogeneous Cement Paste The views...P.O. Box 12211 Research Triangle Park, NC 27709-2211 cement paste, microstructure, RVE modeling, micromechanics REPORT DOCUMENTATION PAGE 11. SPONSOR

  15. Multi-scale gravity field modeling in space and time

    NASA Astrophysics Data System (ADS)

    Wang, Shuo; Panet, Isabelle; Ramillien, Guillaume; Guilloux, Frédéric

    2016-04-01

    The Earth constantly deforms as it undergoes dynamic phenomena, such as earthquakes, post-glacial rebound and water displacement in its fluid envelopes. These processes have different spatial and temporal scales and are accompanied by mass displacements, which create temporal variations of the gravity field. Since 2002, the GRACE satellite missions provide an unprecedented view of the gravity field spatial and temporal variations. Gravity models built from these satellite data are essential to study the Earth's dynamic processes (Tapley et al., 2004). Up to present, time variations of the gravity field are often modelled using spatial spherical harmonics functions averaged over a fixed period, as 10 days or 1 month. This approach is well suited for modeling global phenomena. To better estimate gravity related to local and/or transient processes, such as earthquakes or floods, and adapt the temporal resolution of the model to its spatial resolution, we propose to model the gravity field using localized functions in space and time. For that, we build a model of the gravity field in space and time with a four-dimensional wavelet basis, well localized in space and time. First we design the 4D basis, then, we study the inverse problem to model the gravity field from the potential differences between the twin GRACE satellites, and its regularization using prior knowledge on the water cycle. Our demonstration of surface water mass signals decomposition in time and space is based on the use of synthetic along-track gravitational potential data. We test the developed approach on one year of 4D gravity modeling and compare the reconstructed water heights to those of the input hydrological model. Perspectives of this work is to apply the approach on real GRACE data, addressing the challenge of a realistic noise, to better describe and understand physical processus with high temporal resolution/low spatial resolution or the contrary.

  16. Multi-scale models of cell and tissue dynamics.

    PubMed

    Stolarska, Magdalena A; Kim, Yangjin; Othmer, Hans G

    2009-09-13

    Cell and tissue movement are essential processes at various stages in the life cycle of most organisms. The early development of multi-cellular organisms involves individual and collective cell movement; leukocytes must migrate towards sites of infection as part of the immune response; and in cancer, directed movement is involved in invasion and metastasis. The forces needed to drive movement arise from actin polymerization, molecular motors and other processes, but understanding the cell- or tissue-level organization of these processes that is needed to produce the forces necessary for directed movement at the appropriate point in the cell or tissue is a major challenge. In this paper, we present three models that deal with the mechanics of cells and tissues: a model of an arbitrarily deformable single cell, a discrete model of the onset of tumour growth in which each cell is treated individually, and a hybrid continuum-discrete model of the later stages of tumour growth. While the models are different in scope, their underlying mechanical and mathematical principles are similar and can be applied to a variety of biological systems.

  17. Multi-scale peridynamic modeling of dynamic fracture in concrete

    NASA Astrophysics Data System (ADS)

    Lammi, Christopher; Zhou, Min; Dynamic Properties Research Lab Team

    2015-06-01

    Peridynamics simulations of the dynamic deformation and failure of high-performance concrete are performed at the meso-scale. A pressure-dependent, peridynamic plasticity model and failure criteria are used to capture pressure-sensitive granular flow and fracture. The meso-scale framework explicitly resolves reinforcing phases, pores, and intrinsic flaws. A novel scaling approach is formulated to inform the engineering-scale plasticity model parameters with meso-scale simulation results. The effects of composition, porosity, and fracture energy at the meso-scale on the engineering-scale impact resistance are assessed. The fracture process zone at the meso-scale is found to propagate along adjacent pores and reinforcing phases under tensile and shear loading conditions. The simulations show that tensile strength decreases and dissipation increases as the porosity in the concrete increases. The framework and modeling approach allow the delineation of trends that can be used to design more impact-resistant materials.

  18. Multi-scale peridynamic modeling of dynamic fracture in concrete

    NASA Astrophysics Data System (ADS)

    Lammi, Christopher J.; Zhou, Min

    2017-01-01

    Peridynamics simulations of the dynamic deformation and failure of high-performance concrete are performed at the meso-scale. A pressure-dependent, peridynamic plasticity model and failure criteria are used to capture pressure-sensitive granular flow and fracture. The meso-scale framework explicitly resolves reinforcing phases, pores, and intrinsic flaws. A novel scaling approach is formulated to inform the engineering-scale plasticity model parameters with meso-scale simulation results. The effects of composition, porosity, and fracture energy at the meso-scale on the engineering-scale impact resistance are assessed. The fracture process zone at the meso-scale is found to propagate along adjacent pores and reinforcing phases under tensile and shear loading conditions. The simulations show that tensile strength decreases and dissipation increases as the porosity in the concrete increases. The framework and modeling approach allow the delineation of trends that can be used to design more impact-resistant materials.

  19. Multi-Scale Modeling of Global of Magnetospheric Dynamics

    NASA Technical Reports Server (NTRS)

    Kuznetsova, M. M.; Hesse, M.; Rastatter, L.; Toth, G.; DeZeeuw, D.; Gombosi, T.

    2010-01-01

    To understand the role of magnetic reconnection in global evolution of magnetosphere and to place spacecraft observations into global context it is essential to perform global simulations with physically motivated model of dissipation that is capable to reproduce reconnection rates predicted by kinetic models. In our efforts to bridge the gap between small scale kinetic modeling and global simulations we introduced an approach that allows to quantify the interaction between large-scale global magnetospheric dynamics and microphysical processes in diffusion regions near reconnection sites. We utilized the high resolution global MHD code BATSRUS and incorporate primary mechanism controlling the dissipation in the vicinity of reconnection sites in terms of kinetic corrections to induction and energy equations. One of the key elements of the multiscale modeling of magnetic reconnection is identification of reconnection sites and boundaries of surrounding diffusion regions where non-MHD corrections are required. Reconnection site search in the equatorial plane implemented in our previous studies is extended to cusp and magnetopause reconnection, as well as for magnetotail reconnection in realistic asymmetric configurations. The role of feedback between the non-ideal effects in diffusion regions and global magnetosphere structure and dynamics will be discussed.

  20. Merging Hyperspectural Imagery and Multi Scale Modeling for Laser Lethality

    DTIC Science & Technology

    2016-02-24

    influence of air flow. The models are applied for investigation of the combined effect of the laser energy deposition , chemical reactions, and air flow on the...solid transparent overlayer, (4) the conditions for the formation of nanocrystalline surface layer , sub-surface voids, and frozen surface nanospikes...on providing the physical understanding of the combined effect of the laser energy deposition , chemical reactions, and air flow on the material

  1. Multi-scale modelling for HEDP experiments on Orion

    NASA Astrophysics Data System (ADS)

    Sircombe, N. J.; Ramsay, M. G.; Hughes, S. J.; Hoarty, D. J.

    2016-05-01

    The Orion laser at AWE couples high energy long-pulse lasers with high intensity short-pulses, allowing material to be compressed beyond solid density and heated isochorically. This experimental capability has been demonstrated as a platform for conducting High Energy Density Physics material properties experiments. A clear understanding of the physics in experiments at this scale, combined with a robust, flexible and predictive modelling capability, is an important step towards more complex experimental platforms and ICF schemes which rely on high power lasers to achieve ignition. These experiments present a significant modelling challenge, the system is characterised by hydrodynamic effects over nanoseconds, driven by long-pulse lasers or the pre-pulse of the petawatt beams, and fast electron generation, transport, and heating effects over picoseconds, driven by short-pulse high intensity lasers. We describe the approach taken at AWE; to integrate a number of codes which capture the detailed physics for each spatial and temporal scale. Simulations of the heating of buried aluminium microdot targets are discussed and we consider the role such tools can play in understanding the impact of changes to the laser parameters, such as frequency and pre-pulse, as well as understanding effects which are difficult to observe experimentally.

  2. SLIM: A multi-scale model of the land-sea continuum

    NASA Astrophysics Data System (ADS)

    De Maet, T.; Hanert, E.; Deleersnijder, E.; Fichefet, T.; Legat, V.; Remacle, J. F.; Soares Frazao, S.; Vanclooster, M.; Lambrechts, J.; König Beatty, C.; Bouillon, S.; de Brye, B.; Gourgue, O.; Kärnä, T.; Lietaer, O.; Pestiaux, A.; Slaoui, K.; Thomas, C.

    2012-04-01

    The hydrosphere is made up of a number media, such as the oceans, the shelf seas, the estuaries, the rivers, the land surface and ground water as well as the sea ice - which, for the sake of simplicity, is considered herein to be part of the hydrosphere. The processes taking place in these domains are vastly different in nature and are characterized by a wide range of space- and time-scales. The components of the hydrosphere interact with each other. For instance, the shallow marine and estuarine regions, though accounting for less than 1% of the volume of the oceans, have a biomass far from negligible as compared to that of the oceans, implying that they play a significant role in global biogeochemical cycles. This is one of the reasons why models are now needed that deal with most, if not all, of the components of the hydrospheric system. Numerical models of each of the components of the hydrosphere already exist. However, an integrated model of the whole hydrosphere has yet to be developed. Building such a model is a daunting task, requiring the development of multi-scale/physics simulation tools. Numerical methods for dealing with multi-scale problems are developing rapidly. Unstructured meshes offer an almost infinite geometrical flexibility, allowing the space resolution to be increased when and where necessary. In addition, time steppings for dealing with a wide spectrum of timescales while retaining a high order of accuracy have been developed over recent years (e.g. multi-rate schemes). The Discontinuous Galerkin Finite Element (DGFE) framework SLIM is at his third implementation. It has been build on the GMSH code (http://geuz.org/gmsh), which a state-of-the-art open-source meshing tool. This allows the use of the same definitions and easy interactions between the mesher and the model. Moreover, this provides the same user interface for meshing and visualizing results. It also enables the use of the most recent advances in mesh generation, as GMSH has a

  3. Advanced computations of multi-physics, multi-scale effects in beam dynamics

    SciTech Connect

    Amundson, J.F.; Macridin, A.; Spentzouris, P.; Stern, E.G.; /Fermilab

    2009-01-01

    Current state-of-the-art beam dynamics simulations include multiple physical effects and multiple physical length and/or time scales. We present recent developments in Synergia2, an accelerator modeling framework designed for multi-physics, multi-scale simulations. We summarize recent several recent results in multi-physics beam dynamics, including simulations of three Fermilab accelerators: the Tevatron, the Main Injector and the Debuncher. Early accelerator simulations focused on single-particle dynamics. To a first approximation, the forces on the particles in an accelerator beam are dominated by the external fields due to magnets, RF cavities, etc., so the single-particle dynamics are the leading physical effects. Detailed simulations of accelerators must include collective effects such as the space-charge repulsion of the beam particles, the effects of wake fields in the beam pipe walls and beam-beam interactions in colliders. These simulations require the sort of massively parallel computers that have only become available in recent times. We give an overview of the accelerator framework Synergia2, which was designed to take advantage of the capabilities of modern computational resources and enable simulations of multiple physical effects. We also summarize some recent results utilizing Synergia2 and BeamBeam3d, a tool specialized for beam-beam simulations.

  4. Simulation of Left Atrial Function Using a Multi-Scale Model of the Cardiovascular System

    PubMed Central

    Pironet, Antoine; Dauby, Pierre C.; Paeme, Sabine; Kosta, Sarah; Chase, J. Geoffrey; Desaive, Thomas

    2013-01-01

    During a full cardiac cycle, the left atrium successively behaves as a reservoir, a conduit and a pump. This complex behavior makes it unrealistic to apply the time-varying elastance theory to characterize the left atrium, first, because this theory has known limitations, and second, because it is still uncertain whether the load independence hypothesis holds. In this study, we aim to bypass this uncertainty by relying on another kind of mathematical model of the cardiac chambers. In the present work, we describe both the left atrium and the left ventricle with a multi-scale model. The multi-scale property of this model comes from the fact that pressure inside a cardiac chamber is derived from a model of the sarcomere behavior. Macroscopic model parameters are identified from reference dog hemodynamic data. The multi-scale model of the cardiovascular system including the left atrium is then simulated to show that the physiological roles of the left atrium are correctly reproduced. This include a biphasic pressure wave and an eight-shaped pressure-volume loop. We also test the validity of our model in non basal conditions by reproducing a preload reduction experiment by inferior vena cava occlusion with the model. We compute the variation of eight indices before and after this experiment and obtain the same variation as experimentally observed for seven out of the eight indices. In summary, the multi-scale mathematical model presented in this work is able to correctly account for the three roles of the left atrium and also exhibits a realistic left atrial pressure-volume loop. Furthermore, the model has been previously presented and validated for the left ventricle. This makes it a proper alternative to the time-varying elastance theory if the focus is set on precisely representing the left atrial and left ventricular behaviors. PMID:23755183

  5. Using Multi-Scale Modeling Systems and Satellite Data to Study the Precipitation Processes

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.

    2011-01-01

    In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (l) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, the recent developments and applications of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the precipitating systems and hurricanes/typhoons will be presented. The high-resolution spatial and temporal visualization will be utilized to show the evolution of precipitation processes. Also how to

  6. A multi-scale modeling framework for instabilities of film/substrate systems

    NASA Astrophysics Data System (ADS)

    Xu, Fan; Potier-Ferry, Michel

    2016-01-01

    Spatial pattern formation in stiff thin films on soft substrates is investigated from a multi-scale point of view based on a technique of slowly varying Fourier coefficients. A general macroscopic modeling framework is developed and then a simplified macroscopic model is derived. The model incorporates Asymptotic Numerical Method (ANM) as a robust path-following technique to trace the post-buckling evolution path and to predict secondary bifurcations. The proposed multi-scale finite element framework allows sinusoidal and square checkerboard patterns as well as their bifurcation portraits to be described from a quantitative standpoint. Moreover, it provides an efficient way to compute large-scale instability problems with a significant reduction of computational cost compared to full models.

  7. Multi-scale model of food drying: Current status and challenges.

    PubMed

    Rahman, M M; Joardder, Mohammad U H; Khan, M I H; Nghia, Duc Pham; Karim, M A

    2016-09-19

    For a long time, food engineers have been trying to describe the physical phenomena that occur during food processing especially drying. Physics-based theoretical modeling is an important tool for the food engineers to reduce the hurdles of experimentation. Drying of food is a multi-physics phenomenon such as coupled heat and mass transfer. Moreover, food structure is multi-scale in nature, and the microstructural features play a great role in the food processing specially in drying. Previously simple macroscopic model was used to describe the drying phenomena which can give a little description about the smaller scale. The multiscale modeling technique can handle all the phenomena that occur during drying. In this special kind of modeling approach, the single scale models from bigger to smaller scales are interconnected. With the help of multiscale modeling framework, the transport process associated with drying can be studied on a smaller scale and the resulting information can be transferred to the bigger scale. This article is devoted to discussing the state of the art multi-scale modeling, its prospect and challenges in the field of drying technology. This article has also given some directions to how to overcome the challenges for successful implementation of multi-scale modeling.

  8. Multi-Scale Modeling the Mechanical Properties of Biaxial Weft Knitted Fabrics for Composite Applications

    NASA Astrophysics Data System (ADS)

    Abghary, Mohammad Javad; Nedoushan, Reza Jafari; Hasani, Hossein

    2016-11-01

    In this paper a multi-scale numerical model for simulating the mechanical behavior of biaxial weft knitted fabrics produced based on 1×1 rib structure is presented. Fabrics were produced on a modern flat knitting machine using polyester as stitch yarns and nylon as straight yarns. A macro constitutive equation was presented to model the fabric mechanical behavior as a continuum material. User defined material subroutines were provided to implement the constitutive behavior in Abaqus software. The constitutive equation needs remarkable tensile tests on the fabric as the inputs. To solve this drawbacks meso scale modeling of the fabric was used to predict stress-strain curves of the fabric in three different directions (course, wale and 45°). In these simulations only the yarn properties are needed. To evaluate the accuracy of the proposed macro and meso models, fabric tensile behavior in 22.5 and 67.5° directions were simulated by the calibrated macro model and compared with experimental results. Spherical deformation was also simulated by the multi scale model and compared with experimental results. The results showed that the multi-scale modeling can successfully predict the tensile and spherical deformation of the biaxial weft knitted fabric with least required experiments. This model will be useful for composite applications.

  9. On unified modeling, theory, and method for solving multi-scale global optimization problems

    NASA Astrophysics Data System (ADS)

    Gao, David Yang

    2016-10-01

    A unified model is proposed for general optimization problems in multi-scale complex systems. Based on this model and necessary assumptions in physics, the canonical duality theory is presented in a precise way to include traditional duality theories and popular methods as special applications. Two conjectures on NP-hardness are proposed, which should play important roles for correctly understanding and efficiently solving challenging real-world problems. Applications are illustrated for both nonconvex continuous optimization and mixed integer nonlinear programming.

  10. Integration of regional to outcrop digital data: 3D visualisation of multi-scale geological models

    NASA Astrophysics Data System (ADS)

    Jones, R. R.; McCaffrey, K. J. W.; Clegg, P.; Wilson, R. W.; Holliman, N. S.; Holdsworth, R. E.; Imber, J.; Waggott, S.

    2009-01-01

    Multi-scale geological models contain three-dimensional, spatially referenced data, typically spanning at least six orders of magnitude from outcrop to regional scale. A large number of different geological and geophysical data sources can be combined into a single model. Established 3D visualisation methods that are widely used in hydrocarbon exploration and production for sub-surface data have been adapted for onshore surface geology through a combination of methods for digital data acquisition, 3D visualisation, and geospatial analysis. The integration of georeferenced data across a wider than normal range in scale helps to address several of the existing limitations that are inherent in traditional methods of map production and publishing. The primary advantage of a multi-scale approach is that spatial precision and dimensionality (which are generally degraded when data are displayed in 2D at a single scale) can be preserved at all scales. Real-time, immersive, interactive software, based on a "3D geospatial" graphical user interface (GUI), allows complex geological architectures to be depicted, and is more inherently intuitive than software based on a standard "desktop" GUI metaphor. The continuing convergence of different kinds of geo-modelling, GIS, and visualisation software, as well as industry acceptance of standardised middleware, has helped to make multi-scale geological models a practical reality. This is illustrated with two case studies from NE England and NW Scotland.

  11. Multi-Scale Modeling, Design Strategies and Physical Properties of 2D Composite Sheets

    DTIC Science & Technology

    2015-01-15

    of Pennsylvania. The breakthrough results obtained are 1) prediction and subsequent experimental observation of strain induced changes in electronic...structure of TMD materials 2) Prediction and experimental observation of using defects in 2D materials to enhance charge storage capacity and 3...221 Philadelphia , PA 19104 -6205 4-Mar-2014 ABSTRACT Final Report: 9.4: Multi-scale modeling, design strategies and physical properties of 2D

  12. Physics-Based Multi-Scale Modeling of Shear Initiated Reactions in Energetic and Reactive Materials

    DTIC Science & Technology

    2010-04-01

    Physics-based Multi-scale Modeling of Shear Initiated Reactions in Energetic and Reactive Materials by John K. Brennan, Müge Fermen -Coker...Energetic and Reactive Materials John K. Brennan and Müge Fermen -Coker Weapons and Materials Research Directorate, ARL and Linhbao Tran Shock...Materials 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) John K. Brennan, Müge Fermen -Coker, and Linhbao Tran 5d

  13. Physics-Based Multi-Scale Modeling of Shear Initiated Reactions in Energetic and Reactive Materials

    DTIC Science & Technology

    2009-03-01

    Phys. 1972, 5, 1921. 7. McQuarrie , D. A., Statistical Mechanics , Harper: New York, 1976. 8. Chase, M. W.; Davies, C. A.; Downey, J. R.; Frurip, D. J...munitions due to fragment impact. Present computational capabilities in continuum mechanics codes used by Army designers do not possess the capability to...into the continuum mechanics code CTH, and perform simulations for HEs and RMs. 2 Figure 1. Schematic of multi-scale shear initiation model. As

  14. Capturing remote mixing due to internal tides using multi-scale modeling tool: SOMAR-LES

    NASA Astrophysics Data System (ADS)

    Santilli, Edward; Chalamalla, Vamsi; Scotti, Alberto; Sarkar, Sutanu

    2016-11-01

    Internal tides that are generated during the interaction of an oscillating barotropic tide with the bottom bathymetry dissipate only a fraction of their energy near the generation region. The rest is radiated away in the form of low- high-mode internal tides. These internal tides dissipate energy at remote locations when they interact with the upper ocean pycnocline, continental slope, and large scale eddies. Capturing the wide range of length and time scales involved during the life-cycle of internal tides is computationally very expensive. A recently developed multi-scale modeling tool called SOMAR-LES combines the adaptive grid refinement features of SOMAR with the turbulence modeling features of a Large Eddy Simulation (LES) to capture multi-scale processes at a reduced computational cost. Numerical simulations of internal tide generation at idealized bottom bathymetries are performed to demonstrate this multi-scale modeling technique. Although each of the remote mixing phenomena have been considered independently in previous studies, this work aims to capture remote mixing processes during the life cycle of an internal tide in more realistic settings, by allowing multi-level (coarse and fine) grids to co-exist and exchange information during the time stepping process.

  15. Multi-Scale Modeling of a Graphite-Epoxy-Nanotube System

    NASA Technical Reports Server (NTRS)

    Frankland, S. J. V.; Riddick, J. C.; Gates, T. S.

    2005-01-01

    A multi-scale method is utilized to determine some of the constitutive properties of a three component graphite-epoxy-nanotube system. This system is of interest because carbon nanotubes have been proposed as stiffening and toughening agents in the interlaminar regions of carbon fiber/epoxy laminates. The multi-scale method uses molecular dynamics simulation and equivalent-continuum modeling to compute three of the elastic constants of the graphite-epoxy-nanotube system: C11, C22, and C33. The 1-direction is along the nanotube axis, and the graphene sheets lie in the 1-2 plane. It was found that the C11 is only 4% larger than the C22. The nanotube therefore does have a small, but positive effect on the constitutive properties in the interlaminar region.

  16. Evaluating and Improving Cloud Processes in the Multi-Scale Modeling Framework

    SciTech Connect

    Ackerman, Thomas P.

    2015-03-01

    The research performed under this grant was intended to improve the embedded cloud model in the Multi-scale Modeling Framework (MMF) for convective clouds by using a 2-moment microphysics scheme rather than the single moment scheme used in all the MMF runs to date. The technical report and associated documents describe the results of testing the cloud resolving model with fixed boundary conditions and evaluation of model results with data. The overarching conclusion is that such model evaluations are problematic because errors in the forcing fields control the results so strongly that variations in parameterization values cannot be usefully constrained

  17. Multi-Scale Modeling of an Integrated 3D Braided Composite with Applications to Helicopter Arm

    NASA Astrophysics Data System (ADS)

    Zhang, Diantang; Chen, Li; Sun, Ying; Zhang, Yifan; Qian, Kun

    2017-01-01

    A study is conducted with the aim of developing multi-scale analytical method for designing the composite helicopter arm with three-dimensional (3D) five-directional braided structure. Based on the analysis of 3D braided microstructure, the multi-scale finite element modeling is developed. Finite element analysis on the load capacity of 3D five-directional braided composites helicopter arm is carried out using the software ABAQUS/Standard. The influences of the braiding angle and loading condition on the stress and strain distribution of the helicopter arm are simulated. The results show that the proposed multi-scale method is capable of accurately predicting the mechanical properties of 3D braided composites, validated by the comparison the stress-strain curves of meso-scale RVCs. Furthermore, it is found that the braiding angle is an important factor affecting the mechanical properties of 3D five-directional braided composite helicopter arm. Based on the optimized structure parameters, the nearly net-shaped composite helicopter arm is fabricated using a novel resin transfer mould (RTM) process.

  18. Multi-scale groundwater modelling for the assessment of sustainable borehole yields under drought

    NASA Astrophysics Data System (ADS)

    Upton, Kirsty; Butler, Adrian; Jackson, Chris; Jones, Mike

    2014-05-01

    A new multi-scale groundwater modelling methodology is presented for simulating abstraction boreholes in regional groundwater models. This provides a robust tool for assessing the sustainable yield of supply boreholes, thus improving our understanding of groundwater availability during droughts. The yield of an abstraction well is dependent on a number of factors. These include antecedent recharge and groundwater conditions; the properties of a regional aquifer system; requirements on a groundwater system to maintain river flows or sites of ecological significance; the properties of an individual abstraction borehole; small-scale aquifer heterogeneity around a borehole; the rate of abstraction; and the way in which neighboring abstraction boreholes interact. These factors can all be represented in the multi-scale model, which couples a small-scale radial flow model of an abstraction borehole with a regional-scale groundwater model. The regional groundwater model, ZOOMQ3D, represents the large-scale groundwater system, including lateral and vertical aquifer heterogeneity, rivers, and spatially varying recharge. The 3D radial flow model, SPIDERR, represents linear and non-linear flow to a borehole, local vertical heterogeneity, well storage and pump location. The multi-scale model is applied to a supply borehole (operated by Thames Water) located in the Chalk aquifer within the catchment of the River Thames in southern England. Groundwater abstraction from the Chalk aquifer accounts for 40-70% of the total public water supply in this region. Drought is a recurring feature of the UK climate, and in particular the south and east of England. Since 1850, nine major groundwater droughts have occurred, all of which lasted longer than one year. The most recent occurred in 2010-2012, during which seven water supply companies introduced water usage restrictions, affecting over 20 million people. The radial flow model is initially calibrated against pumping test data from the

  19. The Multi-Scale Model Approach to Thermohydrology at Yucca Mountain

    SciTech Connect

    Glascoe, L; Buscheck, T A; Gansemer, J; Sun, Y

    2002-03-27

    The Multi-Scale Thermo-Hydrologic (MSTH) process model is a modeling abstraction of them1 hydrology (TH) of the potential Yucca Mountain repository at multiple spatial scales. The MSTH model as described herein was used for the Supplemental Science and Performance Analyses (BSC, 2001) and is documented in detail in CRWMS M&O (2000) and Glascoe et al. (2002). The model has been validated to a nested grid model in Buscheck et al. (In Review). The MSTH approach is necessary for modeling thermal hydrology at Yucca Mountain for two reasons: (1) varying levels of detail are necessary at different spatial scales to capture important TH processes and (2) a fully-coupled TH model of the repository which includes the necessary spatial detail is computationally prohibitive. The MSTH model consists of six ''submodels'' which are combined in a manner to reduce the complexity of modeling where appropriate. The coupling of these models allows for appropriate consideration of mountain-scale thermal hydrology along with the thermal hydrology of drift-scale discrete waste packages of varying heat load. Two stages are involved in the MSTH approach, first, the execution of submodels, and second, the assembly of submodels using the Multi-scale Thermohydrology Abstraction Code (MSTHAC). MSTHAC assembles the submodels in a five-step process culminating in the TH model output of discrete waste packages including a mountain-scale influence.

  20. A multi-scale model for correlation in B cell VDJ usage of zebrafish

    NASA Astrophysics Data System (ADS)

    Pan, Keyao; Deem, Michael W.

    2011-10-01

    The zebrafish (Danio rerio) is one of the model animals used for the study of immunology because the dynamics in the adaptive immune system of zebrafish are similar to that in higher animals. In this work, we built a multi-scale model to simulate the dynamics of B cells in the primary and secondary immune responses of zebrafish. We use this model to explain the reported correlation between VDJ usage of B cell repertoires in individual zebrafish. We use a delay ordinary differential equation (ODE) system to model the immune responses in the 6-month lifespan of a zebrafish. This mean field theory gives the number of high-affinity B cells as a function of time during an infection. The sequences of those B cells are then taken from a distribution calculated by a 'microscopic' random energy model. This generalized NK model shows that mature B cells specific to one antigen largely possess a single VDJ recombination. The model allows first-principle calculation of the probability, p, that two zebrafish responding to the same antigen will select the same VDJ recombination. This probability p increases with the B cell population size and the B cell selection intensity. The probability p decreases with the B cell hypermutation rate. The multi-scale model predicts correlations in the immune system of the zebrafish that are highly similar to that from experiment.

  1. Multi-scale modeling of composites subjected to high speed impact

    NASA Astrophysics Data System (ADS)

    Lee, Minhyung; Cha, Myung S.; Kim, Nam H.

    2017-01-01

    In this paper, multi-scale modeling methodology has been applied to simulate the relatively thick composite panels subjected to high speed local impact loading. Instead of massive parallel processing, we propose to use surrogate modeling to bridge micro-scale and macro-scale. Multi-scale modeling of fracture phenomena of composite materials will consist of (1) micro-scale modeling of fiber-matrix structure using the unit-volume-element technique, which can incorporate the boundary effect, and the level set method for crack modeling, which can model the crack propagation independent of finite element mesh; (2) macro-scale simulation of composite panels under high strain-rate impact using material response calculated from micro-scale modeling; and (3) surrogate modeling to integrate the two scales. In order to validate the predictions, first we did the material level lab experiment such as tensile test. We also did the field test of bullet impact into composite panels made of 4 plies fiber. The impact velocity ranges from 300 ˜ 600 m/s.

  2. Multi-scale Modeling of the Cardiovascular System: Disease Development, Progression, and Clinical Intervention.

    PubMed

    Zhang, Yanhang; Barocas, Victor H; Berceli, Scott A; Clancy, Colleen E; Eckmann, David M; Garbey, Marc; Kassab, Ghassan S; Lochner, Donna R; McCulloch, Andrew D; Tran-Son-Tay, Roger; Trayanova, Natalia A

    2016-09-01

    Cardiovascular diseases (CVDs) are the leading cause of death in the western world. With the current development of clinical diagnostics to more accurately measure the extent and specifics of CVDs, a laudable goal is a better understanding of the structure-function relation in the cardiovascular system. Much of this fundamental understanding comes from the development and study of models that integrate biology, medicine, imaging, and biomechanics. Information from these models provides guidance for developing diagnostics, and implementation of these diagnostics to the clinical setting, in turn, provides data for refining the models. In this review, we introduce multi-scale and multi-physical models for understanding disease development, progression, and designing clinical interventions. We begin with multi-scale models of cardiac electrophysiology and mechanics for diagnosis, clinical decision support, personalized and precision medicine in cardiology with examples in arrhythmia and heart failure. We then introduce computational models of vasculature mechanics and associated mechanical forces for understanding vascular disease progression, designing clinical interventions, and elucidating mechanisms that underlie diverse vascular conditions. We conclude with a discussion of barriers that must be overcome to provide enhanced insights, predictions, and decisions in pre-clinical and clinical applications.

  3. A multi-scale method for modeling degradation of bioresorbable polyesters.

    PubMed

    Zhang, Taohong; Zhou, Shaonan; Gao, Xiaohao; Yang, Zhiyong; Sun, Leran; Zhang, Dezheng

    2017-03-01

    A multi-scale model using the cellular automata (CA) and kinetic Monte Carlo (KMC) methods is presented to simulate the degradation process of bioresorbable polyesters such as polylactide (PLA), polyglycolide (PGA) and their copolymers. The model considers the underlying chemical and physical events such as polymer chain scission, oligomer production, crystallization induced by polymer chain scissions, oligomer diffusion and microstructure evolution due to erosion of the small chains. A macroscopic device is discretized into an array of mesoscopic cells. Each cellular lattice is assumed to be made of one polymer chain, which undergoes hydrolysis reaction. The polymer chain scission is modeled using a kinetic Monte Carlo method. Oligomer production, chain crystallization and formation of cavities due to polymer collapse are also modeled on the cellular lattice. Oligomer diffusion is modeled by using Fick's laws at the macroscopic scale. The diffusion coefficient is taken as dependent on the porosity caused by the formation of the cavities. The interactions among the microscopic hydrolysis reaction, mesoscopic formation of cavities and macroscopic diffusion are taken into account. The proposed method forms Multi Scale Cellular Monte Carlo Automata (MS-CMCA). The three-scale approach consists of continuous method and discrete method to deal with certainty problem with underlying stochastic phenomenon. Demonstration examples are provided which show that the model can fit with experimental data in the literature very well.

  4. Multi-Scale Computational Modeling of Two-Phased Metal Using GMC Method

    NASA Technical Reports Server (NTRS)

    Moghaddam, Masoud Ghorbani; Achuthan, A.; Bednacyk, B. A.; Arnold, S. M.; Pineda, E. J.

    2014-01-01

    A multi-scale computational model for determining plastic behavior in two-phased CMSX-4 Ni-based superalloys is developed on a finite element analysis (FEA) framework employing crystal plasticity constitutive model that can capture the microstructural scale stress field. The generalized method of cells (GMC) micromechanics model is used for homogenizing the local field quantities. At first, GMC as stand-alone is validated by analyzing a repeating unit cell (RUC) as a two-phased sample with 72.9% volume fraction of gamma'-precipitate in the gamma-matrix phase and comparing the results with those predicted by finite element analysis (FEA) models incorporating the same crystal plasticity constitutive model. The global stress-strain behavior and the local field quantity distributions predicted by GMC demonstrated good agreement with FEA. High computational saving, at the expense of some accuracy in the components of local tensor field quantities, was obtained with GMC. Finally, the capability of the developed multi-scale model linking FEA and GMC to solve real life sized structures is demonstrated by analyzing an engine disc component and determining the microstructural scale details of the field quantities.

  5. Cloud Feedbacks on Greenhouse Warming in a Multi-Scale Modeling Framework with a Higher-Order Turbulence Closure

    NASA Technical Reports Server (NTRS)

    Cheng, Anning; Xu, Kuan-Man

    2015-01-01

    Five-year simulation experiments with a multi-scale modeling Framework (MMF) with a advanced intermediately prognostic higher-order turbulence closure (IPHOC) in its cloud resolving model (CRM) component, also known as SPCAM-IPHOC (super parameterized Community Atmospheric Model), are performed to understand the fast tropical (30S-30N) cloud response to an instantaneous doubling of CO2 concentration with SST held fixed at present-day values. SPCAM-IPHOC has substantially improved the low-level representation compared with SPCAM. It is expected that the cloud responses to greenhouse warming in SPCAM-IPHOC is more realistic. The change of rising motion, surface precipitation, cloud cover, and shortwave and longwave cloud radiative forcing in SPCAM-IPHOC from the greenhouse warming will be presented in the presentation.

  6. Modelling future impacts of air pollution using the multi-scale UK Integrated Assessment Model (UKIAM).

    PubMed

    Oxley, Tim; Dore, Anthony J; ApSimon, Helen; Hall, Jane; Kryza, Maciej

    2013-11-01

    Integrated assessment modelling has evolved to support policy development in relation to air pollutants and greenhouse gases by providing integrated simulation tools able to produce quick and realistic representations of emission scenarios and their environmental impacts without the need to re-run complex atmospheric dispersion models. The UK Integrated Assessment Model (UKIAM) has been developed to investigate strategies for reducing UK emissions by bringing together information on projected UK emissions of SO2, NOx, NH3, PM10 and PM2.5, atmospheric dispersion, criteria for protection of ecosystems, urban air quality and human health, and data on potential abatement measures to reduce emissions, which may subsequently be linked to associated analyses of costs and benefits. We describe the multi-scale model structure ranging from continental to roadside, UK emission sources, atmospheric dispersion of emissions, implementation of abatement measures, integration with European-scale modelling, and environmental impacts. The model generates outputs from a national perspective which are used to evaluate alternative strategies in relation to emissions, deposition patterns, air quality metrics and ecosystem critical load exceedance. We present a selection of scenarios in relation to the 2020 Business-As-Usual projections and identify potential further reductions beyond those currently being planned.

  7. Advanced in situ multi-scale characterization of hardness of carbon-fiber-reinforced plastic

    NASA Astrophysics Data System (ADS)

    Wang, Hongxin; Masuda, Hideki; Kitazawa, Hideaki; Onishi, Keiko; Kawai, Masamichi; Fujita, Daisuke

    2016-10-01

    In situ multi-scale characterization of hardness of carbon-fiber-reinforced plastic (CFRP) is demonstrated by a traditional hardness tester, instrumented indentation tester and atomic-force-microscope (AFM)-based nanoindentation. In particular, due to the large residual indentation and nonuniform distribution of the microscale carbon fibers, the Vickers hardness could not be calculated by the traditional hardness tester. In addition, the clear residual microindentation could not be formed on the CFRP by instrumented indentation tester because of the large tip half angle of the Berkovich indenter. Therefore, an efficient technique for characterizing the true nanoscale hardness of CFRP was proposed and evaluated. The local hardness of the carbon fibers or plastic matrix on the nanoscale did not vary with nanoindentation location. The Vickers hardnesses of the carbon fiber and plastic matrix determined by AFM-based nanoindentation were 340 ± 30 and 40 ± 2 kgf/mm2, respectively.

  8. APPLICATION OF THE MODELS-3 COMMUNITY MULTI-SCALE AIR QUALITY (CMAQ) MODEL SYSTEM TO SOS/NASHVILLE 1999

    EPA Science Inventory

    The Models-3 Community Multi-scale Air Quality (CMAQ) model, first released by the USEPA in 1999 (Byun and Ching. 1999), continues to be developed and evaluated. The principal components of the CMAQ system include a comprehensive emission processor known as the Sparse Matrix O...

  9. 3D multi-scale modelling of mechanical behaviour of sound and leached mortar

    SciTech Connect

    Bernard, F.; Kamali-Bernard, S. Prince, W.

    2008-04-15

    A 3D multi-scale modelling of mechanical properties of cement-based materials approach is presented. The proposed approach provides a quantitative means to estimate and predict the mechanical properties of cement-based materials taking into account the eventual changes in the micro-structure. Two numerical tools are combined. First, the NIST's 3D model (CEMHYD3D) is used to generate a realistic 3D Representative Volume Element of cement-based materials at different scales. Then, multi-scale simulations are performed by using the FE software Abaqus for the calculation of the mechanical behaviour. The approach is then successfully applied to a specific mortar in order to determine firstly its mechanical behaviour under tensile and compression loadings and secondly the evolution of its Young's modulus under the leaching phenomenon. This evolution is a key parameter since the leaching may be critical for the mechanical integrity of concrete structures such as radioactive waste storage systems in which cement-based materials may be largely used. The numerical results of the modelling are consistent with the experimental ones.

  10. Multi-scale Modeling in Biology: How to Bridge the Gaps between Scales?

    PubMed Central

    Qu, Zhilin; Garfinkel, Alan; Weiss, James N.; Nivala, Melissa

    2011-01-01

    Human physiological functions are regulated across many orders of magnitude in space and time. Integrating the information and dynamics from one scale to another is critical for the understanding of human physiology and the treatment of diseases. Multi-scale modeling, as a computational approach, has been widely adopted by researchers in computational and systems biology. A key unsolved issue is how to represent appropriately the dynamical behaviors of a high-dimensional model of a lower scale by a low-dimensional model of a higher scale, so that it can be used to investigate complex dynamical behaviors at even higher scales of integration. In the article, we first review the widely-used different modeling methodologies and their applications at different scales. We then discuss the gaps between different modeling methodologies and between scales, and discuss potential methods for bridging the gaps between scales. PMID:21704063

  11. Biology meets physics: Reductionism and multi-scale modeling of morphogenesis.

    PubMed

    Green, Sara; Batterman, Robert

    2017-02-01

    A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes a step back in asking whether bottom-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the "tyranny of scales" problem presents a challenge to reductive explanations in both physics and biology. The problem refers to the scale-dependency of physical and biological behaviors that forces researchers to combine different models relying on different scale-specific mathematical strategies and boundary conditions. Analyzing the ways in which different models are combined in multi-scale modeling also has implications for the relation between physics and biology. Contrary to the assumption that physical science approaches provide reductive explanations in biology, we exemplify how inputs from physics often reveal the importance of macro-scale models and explanations. We illustrate this through an examination of the role of biomechanical modeling in developmental biology. In such contexts, the relation between models at different scales and from different disciplines is neither reductive nor completely autonomous, but interdependent.

  12. Multi-scale quantum point contact model for filamentary conduction in resistive random access memories devices

    SciTech Connect

    Lian, Xiaojuan Cartoixà, Xavier; Miranda, Enrique; Suñé, Jordi; Perniola, Luca; Rurali, Riccardo; Long, Shibing; Liu, Ming

    2014-06-28

    We depart from first-principle simulations of electron transport along paths of oxygen vacancies in HfO{sub 2} to reformulate the Quantum Point Contact (QPC) model in terms of a bundle of such vacancy paths. By doing this, the number of model parameters is reduced and a much clearer link between the microscopic structure of the conductive filament (CF) and its electrical properties can be provided. The new multi-scale QPC model is applied to two different HfO{sub 2}-based devices operated in the unipolar and bipolar resistive switching (RS) modes. Extraction of the QPC model parameters from a statistically significant number of CFs allows revealing significant structural differences in the CF of these two types of devices and RS modes.

  13. Multi-scale Modeling Approaches for CO2 Injection, Migration, and Leakage

    NASA Astrophysics Data System (ADS)

    Celia, M.; Nordbotten, J. M.; Gasda, S. E.; Bandilla, K.; Dobossy, M.; Janzen, A.

    2011-12-01

    One of the challenges associated with CO2 storage involves quantitative modeling of the injection, migration, long-term fate, and possible leakage of the CO2 as well as fluids displaced by the injected CO2. Injection into deep saline aquifers involves two-phase flow with interphase mass transfer, strong gravity override, and unfavorable viscosity ratios. The resulting problem can become quite complex, especially when small-scale leakage pathways are involved, or when the flow system needs to be coupled to reactive transport models, geomechanical models, or nonisothermal energy models. Analysis of the characteristic length and time scales associated with each of the important processes and features in the system allows for the development of a multi-scale modeling approach. For example, given the strong buoyancy in the system, vertical stratification of the fluids will occur after a characteristic time. If the simulation time is large compared to that characteristic time scale, then an assumption of stratification, with the corollary assumption of vertical equilibrium for the pressure field, is reasonable. Such an assumption allows the governing equations to be simplified with upscaling defined by vertical integration over the thickness of the formation. Small-scale features such as leakage pathways can be incorporated into the resulting two-dimensional equations via sub-grid-scale analytical (or numerical) solutions for flow dynamics along those features, which can include abandoned wells and localized fault zones. In this way, the overall numerical grid in any permeable formation is always associated with the coarse scale, and local-scale features are embedded into the coarse grid via local solutions defined within the grid cell. These localized leakage pathways are critical to the overall system because they provide high-permeability streaks across caprock formations, thereby connecting permeable formations across the vertical stratigraphic sequence. These

  14. Multi-Scale Modeling of Liquid Phase Sintering Affected by Gravity: Preliminary Analysis

    NASA Technical Reports Server (NTRS)

    Olevsky, Eugene; German, Randall M.

    2012-01-01

    A multi-scale simulation concept taking into account impact of gravity on liquid phase sintering is described. The gravity influence can be included at both the micro- and macro-scales. At the micro-scale, the diffusion mass-transport is directionally modified in the framework of kinetic Monte-Carlo simulations to include the impact of gravity. The micro-scale simulations can provide the values of the constitutive parameters for macroscopic sintering simulations. At the macro-scale, we are attempting to embed a continuum model of sintering into a finite-element framework that includes the gravity forces and substrate friction. If successful, the finite elements analysis will enable predictions relevant to space-based processing, including size and shape and property predictions. Model experiments are underway to support the models via extraction of viscosity moduli versus composition, particle size, heating rate, temperature and time.

  15. Multi-scale modeling of inter-granular fracture in UO2

    SciTech Connect

    Chakraborty, Pritam; Zhang, Yongfeng; Tonks, Michael R.; Biner, S. Bulent

    2015-03-01

    A hierarchical multi-scale approach is pursued in this work to investigate the influence of porosity, pore and grain size on the intergranular brittle fracture in UO2. In this approach, molecular dynamics simulations are performed to obtain the fracture properties for different grain boundary types. A phase-field model is then utilized to perform intergranular fracture simulations of representative microstructures with different porosities, pore and grain sizes. In these simulations the grain boundary fracture properties obtained from molecular dynamics simulations are used. The responses from the phase-field fracture simulations are then fitted with a stress-based brittle fracture model usable at the engineering scale. This approach encapsulates three different length and time scales, and allows the development of microstructurally informed engineering scale model from properties evaluated at the atomistic scale.

  16. Multi-scale modeling of soft fibrous tissues based on proteoglycan mechanics.

    PubMed

    Linka, Kevin; Khiêm, Vu Ngoc; Itskov, Mikhail

    2016-08-16

    Collagen in the form of fibers or fibrils is an essential source of strength and structural integrity in most organs of the human body. Recently, with the help of complex experimental setups, a paradigm change concerning the mechanical contribution of proteoglycans (PGs) took place. Accordingly, PG connections protect the surrounding collagen fibrils from over-stretching rather than transmitting load between them. In this paper, we describe the reported PG mechanics and incorporate it into a multi-scale model of soft fibrous tissues. To this end, a nano-to-micro model of a single collagen fiber is developed by taking the entropic-energetic transition on the collagen molecule level into account. The microscopic damage occurring inside the collagen fiber is elucidated by sliding of PGs as well as by over-stretched collagen molecules. Predictions of this two-constituent-damage model are compared to experimental data available in the literature.

  17. Understanding Prairie Fen Hydrology - a Hierarchical Multi-Scale Groundwater Modeling Approach

    NASA Astrophysics Data System (ADS)

    Sampath, P.; Liao, H.; Abbas, H.; Ma, L.; Li, S.

    2012-12-01

    Prairie fens provide critical habitat to more than 50 rare species and significantly contribute to the biodiversity of the upper Great Lakes region. The sustainability of these globally unique ecosystems, however, requires that they be fed by a steady supply of pristine, calcareous groundwater. Understanding the hydrology that supports the existence of such fens is essential in preserving these valuable habitats. This research uses process-based multi-scale groundwater modeling for this purpose. Two fen-sites, MacCready Fen and Ives Road Fen, in Southern Michigan were systematically studied. A hierarchy of nested steady-state models was built for each fen-site to capture the system's dynamics at spatial scales ranging from the regional groundwater-shed to the local fens. The models utilize high-resolution Digital Elevation Models (DEM), National Hydrologic Datasets (NHD), a recently-assembled water-well database, and results from a state-wide groundwater mapping project to represent the complex hydro-geological and stress framework. The modeling system simulates both shallow glacial and deep bedrock aquifers as well as the interaction between surface water and groundwater. Aquifer heterogeneities were explicitly simulated with multi-scale transition probability geo-statistics. A two-way hydraulic head feedback mechanism was set up between the nested models, such that the parent models provided boundary conditions to the child models, and in turn the child models provided local information to the parent models. A hierarchical mass budget analysis was performed to estimate the seepage fluxes at the surface water/groundwater interfaces and to assess the relative importance of the processes at multiple scales that contribute water to the fens. The models were calibrated using observed base-flows at stream gauging stations and/or static water levels at wells. Three-dimensional particle tracking was used to predict the sources of water to the fens. We observed from the

  18. Fractional-order elastic models of cartilage: A multi-scale approach

    NASA Astrophysics Data System (ADS)

    Magin, Richard L.; Royston, Thomas J.

    2010-03-01

    The objective of this research is to develop new quantitative methods to describe the elastic properties (e.g., shear modulus, viscosity) of biological tissues such as cartilage. Cartilage is a connective tissue that provides the lining for most of the joints in the body. Tissue histology of cartilage reveals a multi-scale architecture that spans a wide range from individual collagen and proteoglycan molecules to families of twisted macromolecular fibers and fibrils, and finally to a network of cells and extracellular matrix that form layers in the connective tissue. The principal cells in cartilage are chondrocytes that function at the microscopic scale by creating nano-scale networks of proteins whose biomechanical properties are ultimately expressed at the macroscopic scale in the tissue's viscoelasticity. The challenge for the bioengineer is to develop multi-scale modeling tools that predict the three-dimensional macro-scale mechanical performance of cartilage from micro-scale models. Magnetic resonance imaging (MRI) and MR elastography (MRE) provide a basis for developing such models based on the nondestructive biomechanical assessment of cartilage in vitro and in vivo. This approach, for example, uses MRI to visualize developing proto-cartilage structure, MRE to characterize the shear modulus of such structures, and fractional calculus to describe the dynamic behavior. Such models can be extended using hysteresis modeling to account for the non-linear nature of the tissue. These techniques extend the existing computational methods to predict stiffness and strength, to assess short versus long term load response, and to measure static versus dynamic response to mechanical loads over a wide range of frequencies (50-1500 Hz). In the future, such methods can perhaps be used to help identify early changes in regenerative connective tissue at the microscopic scale and to enable more effective diagnostic monitoring of the onset of disease.

  19. Multi-scale process and supply chain modelling: from lignocellulosic feedstock to process and products.

    PubMed

    Hosseini, Seyed Ali; Shah, Nilay

    2011-04-06

    There is a large body of literature regarding the choice and optimization of different processes for converting feedstock to bioethanol and bio-commodities; moreover, there has been some reasonable technological development in bioconversion methods over the past decade. However, the eventual cost and other important metrics relating to sustainability of biofuel production will be determined not only by the performance of the conversion process, but also by the performance of the entire supply chain from feedstock production to consumption. Moreover, in order to ensure world-class biorefinery performance, both the network and the individual components must be designed appropriately, and allocation of resources over the resulting infrastructure must effectively be performed. The goal of this work is to describe the key challenges in bioenergy supply chain modelling and then to develop a framework and methodology to show how multi-scale modelling can pave the way to answer holistic supply chain questions, such as the prospects for second generation bioenergy crops.

  20. Validation of Multi-Scale Simulations of the Flow over Big Southern Butte Using Weather Research and Forecasting Model

    NASA Astrophysics Data System (ADS)

    Kosovic, B.; Jimenez, P. A.

    2015-12-01

    Advances in high performance computational resources and frameworks now make possible the use of Numerical Weather Predication (NWP) models for high-resolution simulations of atmospheric flows. In order to develop best practices, standards, and procedures for multi-scale simulations, we need to carry out extensive validation of NWP models across unprecedented range of scales from hundreds of kilometers to tens of meters. However, there are limited observational data available for evaluating high-resolution models. Recently, Nunalee et al (2015) validated large-eddy simulations (LES) using WRF for flow and dispersion based on the Cinder Cone Butte experiment carried out in Idaho in 1982. This study involved moderately complex terrain. We now extend the study to a significantly more complex terrain based on a more recent field study in Idaho. This field study include two experiments: the first one carried out in 2010 and centered on the Big Southern Butte (BSB) and the second in 2011 centered on the Salmon River Canyon both in Idaho (Butler et al., 2015). As a first step, here we focus on using the observations from the BSB experiment to validate multi-scale simulations using the WRF model. We carry out both mesoscale simulations and large-eddy simulations (LES). Nested mesoscale simulations are carried out using the innermost nest with grid cell size of 300m while nested WRF-LES are carried with grid cell size of ~50m. We analyze the performance of PBL scheme in mesoscale simulations and the resulting interplay between subgrid parameterization and numerical advection scheme in LES. The results of this analysis are used to assess performance of PBL schemes in complex terrain where the assumption of horizontal homogeneity on which these schemes are based are violated and to suggest the modifications to PBL scheme to account for the effect of heterogeneity.

  1. Evaluation and improvement of the cloud resolving model component of the multi-scale modeling framework

    SciTech Connect

    Xu, Kuan-Man; Cheng, Anning

    2009-10-01

    Developed, implemented and tested an improved Colorado State University (CSU) SAM (System for Atmospheric Modeling) cloud-resolving model (CRM) with the advanced third-order turbulence closure (IPHOC).

  2. Land-Atmosphere Coupling in the Multi-Scale Modelling Framework

    NASA Astrophysics Data System (ADS)

    Kraus, P. M.; Denning, S.

    2015-12-01

    The Multi-Scale Modeling Framework (MMF), in which cloud-resolving models (CRMs) are embedded within general circulation model (GCM) gridcells to serve as the model's cloud parameterization, has offered a number of benefits to GCM simulations. The coupling of these cloud-resolving models directly to land surface model instances, rather than passing averaged atmospheric variables to a single instance of a land surface model, the logical next step in model development, has recently been accomplished. This new configuration offers conspicuous improvements to estimates of precipitation and canopy through-fall, but overall the model exhibits warm surface temperature biases and low productivity.This work presents modifications to a land-surface model that take advantage of the new multi-scale modeling framework, and accommodate the change in spatial scale from a typical GCM range of ~200 km to the CRM grid-scale of 4 km.A parameterization is introduced to apportion modeled surface radiation into direct-beam and diffuse components. The diffuse component is then distributed among the land-surface model instances within each GCM cell domain. This substantially reduces the number excessively low light values provided to the land-surface model when cloudy conditions are modeled in the CRM, associated with its 1-D radiation scheme. The small spatial scale of the CRM, ~4 km, as compared with the typical ~200 km GCM scale, provides much more realistic estimates of precipitation intensity, this permits the elimination of a model parameterization of canopy through-fall. However, runoff at such scales can no longer be considered as an immediate flow to the ocean. Allowing sub-surface water flow between land-surface instances within the GCM domain affords better realism and also reduces temperature and productivity biases.The MMF affords a number of opportunities to land-surface modelers, providing both the advantages of direct simulation at the 4 km scale and a much reduced

  3. Multi-scale model analysis and hindcast of the 2013 Colorado Flood

    NASA Astrophysics Data System (ADS)

    Gochis, David; Yu, Wei; Sampson, Kevin; Dugger, Aubrey; McCreight, James; Zhang, Yongxin; Ikeda, Kyoko

    2015-04-01

    While the generation of most flood and flash flood events is fundamentally linked to the occurrence of heavy rainfall, the physical mechanisms responsible for translating rainfall into floods are complex and manifold. These runoff generation processes evolve over many spatial and temporal scales during the course of flooding events. As such robust flood and flash flood prediction systems need to account for multitude of terrestrial processes occurring over a wide range of space and time scales. One such extreme multiscale flood event was the 2013 Colorado Flood in which over 400 mm of rainfall fell along the Rock Mountain mountain front region over the course of a few days. The flooding impacts from this heavy rainfall event included not only high, fast flows in steep mountain streams but also included large areas of inundation on the adjacent plains and numerous soil saturation excess impacts such as hillslope failures and groundwater intrusions into domestic structures. A multi-scale and multi-process evaluation of this flood event is performed using the community WRF-Hydro modeling system. We incorporate several operational quantitative precipitation estimate and quantitative precipitation forecast products in the analysis and document the skill of multiple configurations of WRF-Hydro physics options across a range of contributing area length scales. Emphasis is placed on assessing how well the different model configurations capture the multi-scale streamflow response from small headwater catchments out to the entire South Platte River basin whose total contributing area exceeds 25,000 sq km. In addition to streamflow we also present evaluations of event simulations and hindcasts of soil saturation fraction, groundwater levels and inundated areas as a means of assessing different runoff generation mechanisms. Finally, results from a U.S. national-scale, fully-coupled hydrometeorological hindcast of the 2013 Colorado flood event using the combined WRF atmospheric

  4. Optimal design of laminated-MRE bearings with multi-scale model

    NASA Astrophysics Data System (ADS)

    Chen, Shiwei; Wang, Xiaojie; Zhang, Ze; Mu, Wenjun; Li, Rui

    2016-10-01

    In the design of a laminated magneto-rheological elastomeric bearing (MREB), the passive rubbers are replaced with composite layers of rubber and MREs. The applied magnetic field, produced by the built-in electromagnet through the input current, changes the stiffness and damping of MREs, and thus that of the device. Typically, a good MREB should possess higher adjustable properties with less activating power in avoiding overheating problem. Thus an optimized design of MREB should integrate the MRE material design into mechanical and electromagnetic components to achieve a trade-off between power consumption and adjustability of stiffness. In this study, we propose a method to analyze and design a laminated MRE bearing, in which the optimal parameters of materials and mechanical structure of the MRE bearing are determined. Based on the multi-scale and magneto-mechanical coupling theories, we establish a multi-scale model for the MRE bearing considering the influence of particle volume fraction, particle distribution, and thickness of MRE laminated layers on its mechanical performance. Within the micro-scale analysis, the representative volume unit is used to address the effect of particle volume fraction and distribution on mechanical and magnetic properties of MRE itself. Within the macro-scale analysis, we build both mechanical and magnetic models for the laminated MRE bearing. Based on the theoretical analysis, a laminated MRE bearing with four-layer MRE is designed and fabricated. The performance of the MRE bearing has been tested by using MTS test bench. The results are compared with that of model analysis. Both experimental and theoretical results indicate that optimal design of MREB depends on the MRE’s particle volume fraction which is related with MREB’s input power limitation.

  5. Multi-scale model for the hierarchical architecture of native cellulose hydrogels.

    PubMed

    Martínez-Sanz, Marta; Mikkelsen, Deirdre; Flanagan, Bernadine; Gidley, Michael J; Gilbert, Elliot P

    2016-08-20

    The structure of protiated and deuterated cellulose hydrogels has been investigated using a multi-technique approach combining small-angle scattering with diffraction, spectroscopy and microscopy. A model for the multi-scale structure of native cellulose hydrogels is proposed which highlights the essential role of water at different structural levels characterised by: (i) the existence of cellulose microfibrils containing an impermeable crystalline core surrounded by a partially hydrated paracrystalline shell, (ii) the creation of a strong network of cellulose microfibrils held together by hydrogen bonding to form cellulose ribbons and (iii) the differential behaviour of tightly bound water held within the ribbons compared to bulk solvent. Deuterium labelling provides an effective platform on which to further investigate the role of different plant cell wall polysaccharides in cellulose composite formation through the production of selectively deuterated cellulose composite hydrogels.

  6. Efficient formulation of scale separation for multi-scale modeling of interfacial flows

    NASA Astrophysics Data System (ADS)

    Luo, J.; Hu, X. Y.; Adams, N. A.

    2016-03-01

    We propose an efficient formulation of the scale-separation approach which has been developed by Han et al. [10] for multi-scale sharp interface modeling of multi-phase flows based on the level-set technique. Instead of shifting the entire level-set field twice as in the original method, the improved method identifies the non-resolved interface structures from two auxiliary level-sets close to the interface. Non-resolved structures are separated from the interface by a localized re-distancing method, which increases the computational efficiency considerably compared to the original global reinitialization procedure. Several tests for two-phase flow problems, involving simple and complex interface structures, are carried out to show that the present method maintains sharper interface structures than the original method, and achieves effective scale-separation.

  7. CMAQ (Community Multi-Scale Air Quality) atmospheric distribution model adaptation to region of Hungary

    NASA Astrophysics Data System (ADS)

    Lázár, Dóra; Weidinger, Tamás

    2016-04-01

    For our days, it has become important to measure and predict the concentration of harmful atmospheric pollutants such as dust, aerosol particles of different size ranges, nitrogen compounds, and ozone. The Department of Meteorology at Eötvös Loránd University has been applying the WRF (Weather Research and Forecasting) model several years ago, which is suitable for weather forecasting tasks and provides input data for various environmental models (e.g. DNDC). By adapting the CMAQ (Community Multi-scale Air Quality) model we have designed a combined ambient air-meteorological model (WRF-CMAQ). In this research it is important to apply different emission databases and a background model describing the initial distribution of the pollutant. We used SMOKE (Sparse Matrix Operator Kernel Emissions) model for construction emission dataset from EMEP (European Monitoring and Evaluation Programme) inventories and GEOS-Chem model for initial and boundary conditions. Our model settings were CMAQ CB05 (Carbon Bond 2005) chemical mechanism with 108 x 108 km, 36 x 36 km and 12 x 12 km grids for regions of Europe, the Carpathian Basin and Hungary respectively. i) The structure of the model system, ii) a case study for Carpathian Basin (an anticyclonic weather situation at 21th September 2012) are presented. iii) Verification of ozone forecast has been provided based on the measurements of background air pollution stations. iv) Effects of model attributes (f.e. transition time, emission dataset, parameterizations) for the ozone forecast in Hungary are also investigated.

  8. YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.

    PubMed

    Tan, Robert K Z; Petrov, Anton S; Harvey, Stephen C

    2006-05-01

    Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created YUP, a general-purpose program for coarse-grained and multi-scaled models. YUP extends the Python programming language by adding new data types. We have then used the extended language to implement three classes of coarse-grained models. The coarse-grained RNA model type is an unusual non-linear polymer and the assembly was easily handled with a simple program. The molecular dynamics algorithm had to be extended for a coarse-grained DNA model so that it could detect a failure that is invisible to a standard implementation. A third model type took advantage of access to the force field to simulate the packing of DNA in viral capsid. We find that objects are easy to modify, extend and redeploy. Thus, new classes of coarse-grained models can be implemented easily.

  9. Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

    PubMed Central

    Cilfone, Nicholas A.; Kirschner, Denise E.; Linderman, Jennifer J.

    2015-01-01

    Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level. PMID:26366228

  10. Towards Characterization, Modeling, and Uncertainty Quantification in Multi-scale Mechanics of Oragnic-rich Shales

    NASA Astrophysics Data System (ADS)

    Abedi, S.; Mashhadian, M.; Noshadravan, A.

    2015-12-01

    Increasing the efficiency and sustainability in operation of hydrocarbon recovery from organic-rich shales requires a fundamental understanding of chemomechanical properties of organic-rich shales. This understanding is manifested in form of physics-bases predictive models capable of capturing highly heterogeneous and multi-scale structure of organic-rich shale materials. In this work we present a framework of experimental characterization, micromechanical modeling, and uncertainty quantification that spans from nanoscale to macroscale. Application of experiments such as coupled grid nano-indentation and energy dispersive x-ray spectroscopy and micromechanical modeling attributing the role of organic maturity to the texture of the material, allow us to identify unique clay mechanical properties among different samples that are independent of maturity of shale formations and total organic content. The results can then be used to inform the physically-based multiscale model for organic rich shales consisting of three levels that spans from the scale of elementary building blocks (e.g. clay minerals in clay-dominated formations) of organic rich shales to the scale of the macroscopic inorganic/organic hard/soft inclusion composite. Although this approach is powerful in capturing the effective properties of organic-rich shale in an average sense, it does not account for the uncertainty in compositional and mechanical model parameters. Thus, we take this model one step forward by systematically incorporating the main sources of uncertainty in modeling multiscale behavior of organic-rich shales. In particular we account for the uncertainty in main model parameters at different scales such as porosity, elastic properties and mineralogy mass percent. To that end, we use Maximum Entropy Principle and random matrix theory to construct probabilistic descriptions of model inputs based on available information. The Monte Carlo simulation is then carried out to propagate the

  11. multi-scale approaches for full waveform difference inversion and tomographic model analysis

    NASA Astrophysics Data System (ADS)

    Yuan, Y.; Simons, F. J.; Luo, Y.

    2012-12-01

    Tomographic Earth models are solutions to mixed-determined inverse problems, which are formulated to minimize some measure of difference between synthetics and observed data. Typically, the measurement takes the form of a cross-correlation travel-time difference, or it might be the norm of the difference between the entire waveforms, in which case every wiggle is being used to extract information from the data. Full-waveform difference tomography suffers from a slow convergence rate and a danger of converging to local minima. In this presentation, we explore several routes to improving full-waveform inversion strategies for global and regional seismic tomography. First, we will discuss a wavelet-based multi-scale approach that works progressively from low to higher scales, step-by-step involving more details of the waveform. Second, we will discuss a hybrid misfit strategy that combines cross-correlation traveltime and waveform-difference measurements. We will discuss the making of multiscale sensitivity kernels using wavelet decompositions of the seismogram. Lastly, we move to the model space to conduct a multi-scale analysis of global tomographic models using a class of 3-D spherical wavelet bases that are implemented on the ``cubed ball'', the 3-D extension of the ``cubed sphere''. Using this novel transform we study the sparsity of global seismic tomographic models via thresholded reconstruction, and characterize the relative importance and patterns of features in the Earth models via individual and cumulative reconstructions of their wavelet coefficients. Whether on the side of the data, the sensitivity kernels, or in the model space, tomographic inverse problems have much to gain from the flexibility of the wavelet decomposition in one, two and three dimensions, and this on a global, regional or exploration scale, as we show by example. Full waveform difference inversion. The first figure shows our target model with two anomalous regions. The red stars

  12. A multi scale multi-dimensional thermo electrochemical modelling of high capacity lithium-ion cells

    NASA Astrophysics Data System (ADS)

    Tourani, Abbas; White, Peter; Ivey, Paul

    2014-06-01

    Lithium iron phosphate (LFP) and lithium manganese oxide (LMO) are competitive and complementary to each other as cathode materials for lithium-ion batteries, especially for use in electric vehicles. A multi scale multi-dimensional physic-based model is proposed in this paper to study the thermal behaviour of the two lithium-ion chemistries. The model consists of two sub models, a one dimensional (1D) electrochemical sub model and a two dimensional (2D) thermo-electric sub model, which are coupled and solved concurrently. The 1D model predicts the heat generation rate (Qh) and voltage (V) of the battery cell through different load cycles. The 2D model of the battery cell accounts for temperature distribution and current distribution across the surface of the battery cell. The two cells are examined experimentally through 90 h load cycles including high/low charge/discharge rates. The experimental results are compared with the model results and they are in good agreement. The presented results in this paper verify the cells temperature behaviour at different operating conditions which will lead to the design of a cost effective thermal management system for the battery pack.

  13. A Multi-Scale Modeling Framework for Individualized, Spatiotemporal Prediction of Drug Effects and Toxicological Risk

    PubMed Central

    Diaz Ochoa, Juan G.; Bucher, Joachim; Péry, Alexandre R. R.; Zaldivar Comenges, José M.; Niklas, Jens; Mauch, Klaus

    2013-01-01

    In this study, we focus on a novel multi-scale modeling approach for spatiotemporal prediction of the distribution of substances and resulting hepatotoxicity by combining cellular models, a 2D liver model, and whole body model. As a case study, we focused on predicting human hepatotoxicity upon treatment with acetaminophen based on in vitro toxicity data and potential inter-individual variability in gene expression and enzyme activities. By aggregating mechanistic, genome-based in silico cells to a novel 2D liver model and eventually to a whole body model, we predicted pharmacokinetic properties, metabolism, and the onset of hepatotoxicity in an in silico patient. Depending on the concentration of acetaminophen in the liver and the accumulation of toxic metabolites, cell integrity in the liver as a function of space and time as well as changes in the elimination rate of substances were estimated. We show that the variations in elimination rates also influence the distribution of acetaminophen and its metabolites in the whole body. Our results are in agreement with experimental results. What is more, the integrated model also predicted variations in drug toxicity depending on alterations of metabolic enzyme activities. Variations in enzyme activity, in turn, reflect genetic characteristics or diseases of individuals. In conclusion, this framework presents an important basis for efficiently integrating inter-individual variability data into models, paving the way for personalized or stratified predictions of drug toxicity and efficacy. PMID:23346056

  14. Multi-scale modeling of urban air pollution: development of a Street-in-Grid model

    NASA Astrophysics Data System (ADS)

    Kim, Youngseob; Wu, You; Seigneur, Christian; Roustan, Yelva

    2016-04-01

    A new multi-scale model of urban air pollution is presented. This model combines a chemical-transport model (CTM) that includes a comprehensive treatment of atmospheric chemistry and transport at spatial scales greater than 1 km and a street-network model that describes the atmospheric concentrations of pollutants in an urban street network. The street-network model is based on the general formulation of the SIRANE model and consists of two main components: a street-canyon component and a street-intersection component. The street-canyon component calculates the mass transfer velocity at the top of the street canyon (roof top) and the mean wind velocity within the street canyon. The estimation of the mass transfer velocity depends on the intensity of the standard deviation of the vertical velocity at roof top. The effect of various formulations of this mass transfer velocity on the pollutant transport at roof-top level is examined. The street-intersection component calculates the mass transfer from a given street to other streets across the intersection. These mass transfer rates among the streets are calculated using the mean wind velocity calculated for each street and are balanced so that the total incoming flow rate is equal to the total outgoing flow rate from the intersection including the flow between the intersection and the overlying atmosphere at roof top. In the default option, the Leighton photostationary cycle among ozone (O3) and nitrogen oxides (NO and NO2) is used to represent the chemical reactions within the street network. However, the influence of volatile organic compounds (VOC) on the pollutant concentrations increases when the nitrogen oxides (NOx) concentrations are low. To account for the possible VOC influence on street-canyon chemistry, the CB05 chemical kinetic mechanism, which includes 35 VOC model species, is implemented in this street-network model. A sensitivity study is conducted to assess the uncertainties associated with the use of

  15. An Eye Model for Computational Dosimetry Using A Multi-Scale Voxel Phantom

    NASA Astrophysics Data System (ADS)

    Caracappa, Peter F.; Rhodes, Ashley; Fiedler, Derek

    2014-06-01

    The lens of the eye is a radiosensitive tissue with cataract formation being the major concern. Recently reduced recommended dose limits to the lens of the eye have made understanding the dose to this tissue of increased importance. Due to memory limitations, the voxel resolution of computational phantoms used for radiation dose calculations is too large to accurately represent the dimensions of the eye. A revised eye model is constructed using physiological data for the dimensions of radiosensitive tissues, and is then transformed into a high-resolution voxel model. This eye model is combined with an existing set of whole body models to form a multi-scale voxel phantom, which is used with the MCNPX code to calculate radiation dose from various exposure types. This phantom provides an accurate representation of the radiation transport through the structures of the eye. Two alternate methods of including a high-resolution eye model within an existing whole body model are developed. The accuracy and performance of each method is compared against existing computational phantoms.

  16. Multi-scale model for hepatitis C viral load kinetics under treatment with direct acting antivirals.

    PubMed

    Clausznitzer, Diana; Harnisch, Julia; Kaderali, Lars

    2016-06-15

    Hepatitis C virus (HCV) infections are a global health problem, and extensive research over the last decades has been targeted at understanding its molecular biology and developing effective antiviral treatments. Recently, a number of potent direct acting antiviral drugs have been developed targeting specific processes in the viral life cycle. Here, we developed a mathematical multi-scale model of the within-host dynamics of HCV infection by integrating a standard model for viral infection with a detailed model of the viral replication cycle inside infected cells. We use this model to study patient time courses of viral load under treatment with daclatasvir, an inhibitor of the viral non-structural protein NS5A. Model analysis predicts that treatment efficacy can be increased by combining daclatasvir with dedicated viral polymerase inhibitors, corresponding to promising current strategies in drug development. Hence, our model presents a predictive tool for in silico simulations, which can be used to study and optimize direct acting antiviral drug treatment.

  17. Multi-scale modelling of ovarian follicular development: From follicular morphogenesis to selection for ovulation.

    PubMed

    Monniaux, Danielle; Michel, Philippe; Postel, Marie; Clément, Frédérique

    2016-06-01

    In this review, we present multi-scale mathematical models of ovarian follicular development that are based on the embedding of physiological mechanisms into the cell scale. During basal follicular development, follicular growth operates through an increase in the oocyte size concomitant with the proliferation of its surrounding granulosa cells. We have developed a spatio-temporal model of follicular morphogenesis explaining how the interactions between the oocyte and granulosa cells need to be properly balanced to shape the follicle. During terminal follicular development, the ovulatory follicle is selected amongst a cohort of simultaneously growing follicles. To address this process of follicle selection, we have developed a model giving a continuous and deterministic description of follicle development, adapted to high numbers of cells and based on the dynamical and hormonally regulated repartition of granulosa cells into different cell states, namely proliferation, differentiation and apoptosis. This model takes into account the hormonal feedback loop involving the growing ovarian follicles and the pituitary gland, and enables the exploration of mechanisms regulating the number of ovulations at each ovarian cycle. Both models are useful for addressing ovarian physio-pathological situations. Moreover, they can be proposed as generic modelling environments to study various developmental processes and cell interaction mechanisms.

  18. On the computation of a retina resistivity profile for applications in multi-scale modeling of electrical stimulation and absorption.

    PubMed

    Loizos, Kyle; RamRakhyani, Anil Kumar; Anderson, James; Marc, Robert; Lazzi, Gianluca

    2016-06-21

    This study proposes a methodology for computationally estimating resistive properties of tissue in multi-scale computational models, used for studying the interaction of electromagnetic fields with neural tissue, with applications to both dosimetry and neuroprosthetics. Traditionally, models at bulk tissue- and cellular-level scales are solved independently, linking resulting voltage from existing resistive tissue-scale models as extracellular sources to cellular models. This allows for solving the effects that external electric fields have on cellular activity. There are two major limitations to this approach: first, the resistive properties of the tissue need to be chosen, of which there are contradicting measurements in literature; second, the measurements of resistivity themselves may be inaccurate, leading to the mentioned contradicting results found across different studies. Our proposed methodology allows for constructing computed resistivity profiles using knowledge of only the neural morphology within the multi-scale model, resulting in a practical implementation of the effective medium theory; this bypasses concerns regarding the choice of resistive properties and accuracy of measurement setups. A multi-scale model of retina is constructed with an external electrode to serve as a test bench for analyzing existing and resulting resistivity profiles, and validation is presented through the reconstruction of a published resistivity profile of retina tissue. Results include a computed resistivity profile of retina tissue for use with a retina multi-scale model used to analyze effects of external electric fields on neural activity.

  19. On the computation of a retina resistivity profile for applications in multi-scale modeling of electrical stimulation and absorption

    NASA Astrophysics Data System (ADS)

    Loizos, Kyle; RamRakhyani, Anil Kumar; Anderson, James; Marc, Robert; Lazzi, Gianluca

    2016-06-01

    This study proposes a methodology for computationally estimating resistive properties of tissue in multi-scale computational models, used for studying the interaction of electromagnetic fields with neural tissue, with applications to both dosimetry and neuroprosthetics. Traditionally, models at bulk tissue- and cellular-level scales are solved independently, linking resulting voltage from existing resistive tissue-scale models as extracellular sources to cellular models. This allows for solving the effects that external electric fields have on cellular activity. There are two major limitations to this approach: first, the resistive properties of the tissue need to be chosen, of which there are contradicting measurements in literature; second, the measurements of resistivity themselves may be inaccurate, leading to the mentioned contradicting results found across different studies. Our proposed methodology allows for constructing computed resistivity profiles using knowledge of only the neural morphology within the multi-scale model, resulting in a practical implementation of the effective medium theory; this bypasses concerns regarding the choice of resistive properties and accuracy of measurement setups. A multi-scale model of retina is constructed with an external electrode to serve as a test bench for analyzing existing and resulting resistivity profiles, and validation is presented through the reconstruction of a published resistivity profile of retina tissue. Results include a computed resistivity profile of retina tissue for use with a retina multi-scale model used to analyze effects of external electric fields on neural activity.

  20. On the computation of a retina resistivity profile for applications in multi-scale modeling of electrical stimulation and absorption

    PubMed Central

    Loizos, Kyle; RamRakhyani, Anil Kumar; Anderson, James; Marc, Robert; Lazzi, Gianluca

    2016-01-01

    This study proposes a methodology for computationally estimating resistive properties of tissue in multi-scale computational models, used for studying the interaction of electromagnetic fields with neural tissue, with applications to both dosimetry and neuroprosthetics. Traditionally, models at bulk tissue- and cellular-level scales are solved independently, linking resulting voltage from existing resistive tissue-scale models as extracellular sources to cellular models. This allows for solving the effects that external electric fields have on cellular activity. There are two major limitations to this approach: first, the resistive properties of the tissue need to be chosen, of which there are contradicting measurements in literature; second, the measurements of resistivity themselves may be inaccurate, leading to the mentioned contradicting results found across different studies. Our proposed methodology allows for constructing computed resistivity profiles using knowledge of only the neural morphology within the multi-scale model, resulting in a practical implementation of the effective medium theory; this bypasses concerns regarding the choice of resistive properties and accuracy of measurement setups. A multi-scale model of retina is constructed with an external electrode to serve as a test bench for analyzing existing and resulting resistivity profiles, and validation is presented through the reconstruction of a published resistivity profile of retina tissue. Results include a computed resistivity profile of retina tissue for use with a retina multi-scale model used to analyze effects of external electric fields on neural activity. PMID:27223656

  1. A dissipation-based control method for the multi-scale modelling of quasi-brittle materials

    NASA Astrophysics Data System (ADS)

    Massart, Thierry J.; Peerlings, Ron H. J.; Geers, Marc G. D.

    2005-07-01

    Multi-scale models based on computational homogenisation are nowadays developed for the simulation of complex material behaviour. The use of homogenisation techniques on finite-sized representative volume elements in the presence of quasi-brittle damage may lead to the presence of snap-backs in the macroscopic material response. A methodology to simulate this type of response in the multi-scale technique is proposed, based on the control of the dissipation at the mesoscopic scale. To cite this article: T.J. Massart et al., C. R. Mecanique 333 (2005).

  2. A multi-scale modelling procedure to quantify hydrological impacts of upland land management

    NASA Astrophysics Data System (ADS)

    Wheater, H. S.; Jackson, B.; Bulygina, N.; Ballard, C.; McIntyre, N.; Marshall, M.; Frogbrook, Z.; Solloway, I.; Reynolds, B.

    2008-12-01

    Recent UK floods have focused attention on the effects of agricultural intensification on flood risk. However, quantification of these effects raises important methodological issues. Catchment-scale data have proved inadequate to support analysis of impacts of land management change, due to climate variability, uncertainty in input and output data, spatial heterogeneity in land use and lack of data to quantify historical changes in management practices. Manipulation experiments to quantify the impacts of land management change have necessarily been limited and small scale, and in the UK mainly focused on the lowlands and arable agriculture. There is a need to develop methods to extrapolate from small scale observations to predict catchment-scale response, and to quantify impacts for upland areas. With assistance from a cooperative of Welsh farmers, a multi-scale experimental programme has been established at Pontbren, in mid-Wales, an area of intensive sheep production. The data have been used to support development of a multi-scale modelling methodology to assess impacts of agricultural intensification and the potential for mitigation of flood risk through land use management. Data are available from replicated experimental plots under different land management treatments, from instrumented field and hillslope sites, including tree shelter belts, and from first and second order catchments. Measurements include climate variables, soil water states and hydraulic properties at multiple depths and locations, tree interception, overland flow and drainflow, groundwater levels, and streamflow from multiple locations. Fine resolution physics-based models have been developed to represent soil and runoff processes, conditioned using experimental data. The detailed models are used to calibrate simpler 'meta- models' to represent individual hydrological elements, which are then combined in a semi-distributed catchment-scale model. The methodology is illustrated using field

  3. A semi-analytical model for the flow behavior of naturally fractured formations with multi-scale fracture networks

    NASA Astrophysics Data System (ADS)

    Jia, Pin; Cheng, Linsong; Huang, Shijun; Wu, Yonghui

    2016-06-01

    This paper presents a semi-analytical model for the flow behavior of naturally fractured formations with multi-scale fracture networks. The model dynamically couples an analytical dual-porosity model with a numerical discrete fracture model. The small-scale fractures with the matrix are idealized as a dual-porosity continuum and an analytical flow solution is derived based on source functions in Laplace domain. The large-scale fractures are represented explicitly as the major fluid conduits and the flow is numerically modeled, also in Laplace domain. This approach allows us to include finer details of the fracture network characteristics while keeping the computational work manageable. For example, the large-scale fracture network may have complex geometry and varying conductivity, and the computations can be done at predetermined, discrete times, without any grids in the dual-porosity continuum. The validation of the semi-analytical model is demonstrated in comparison to the solution of ECLIPSE reservoir simulator. The simulation is fast, gridless and enables rapid model setup. On the basis of the model, we provide detailed analysis of the flow behavior of a horizontal production well in fractured reservoir with multi-scale fracture networks. The study has shown that the system may exhibit six flow regimes: large-scale fracture network linear flow, bilinear flow, small-scale fracture network linear flow, pseudosteady-state flow, interporosity flow and pseudoradial flow. During the first four flow periods, the large-scale fracture network behaves as if it only drains in the small-scale fracture network; that is, the effect of the matrix is negligibly small. The characteristics of the bilinear flow and the small-scale fracture network linear flow are predominantly determined by the dimensionless large-scale fracture conductivity. And low dimensionless fracture conductivity will generate large pressure drops in the large-scale fractures surrounding the wellbore. With

  4. Progression to multi-scale models and the application to food system intervention strategies.

    PubMed

    Gröhn, Yrjö T

    2015-02-01

    The aim of this article is to discuss how the systems science approach can be used to optimize intervention strategies in food animal systems. It advocates the idea that the challenges of maintaining a safe food supply are best addressed by integrating modeling and mathematics with biological studies critical to formulation of public policy to address these challenges. Much information on the biology and epidemiology of food animal systems has been characterized through single-discipline methods, but until now this information has not been thoroughly utilized in a fully integrated manner. The examples are drawn from our current research. The first, explained in depth, uses clinical mastitis to introduce the concept of dynamic programming to optimize management decisions in dairy cows (also introducing the curse of dimensionality problem). In the second example, a compartmental epidemic model for Johne's disease with different intervention strategies is optimized. The goal of the optimization strategy depends on whether there is a relationship between Johne's and Crohn's disease. If so, optimization is based on eradication of infection; if not, it is based on the cow's performance only (i.e., economic optimization, similar to the mastitis example). The third example focuses on food safety to introduce risk assessment using Listeria monocytogenes and Salmonella Typhimurium. The last example, practical interventions to effectively manage antibiotic resistance in beef and dairy cattle systems, introduces meta-population modeling that accounts for bacterial growth not only in the host (cow), but also in the cow's feed, drinking water and the housing environment. Each example stresses the need to progress toward multi-scale modeling. The article ends with examples of multi-scale systems, from food supply systems to Johne's disease. Reducing the consequences of foodborne illnesses (i.e., minimizing disease occurrence and associated costs) can only occur through an

  5. Multi-scale analysis of optic chiasmal compression by finite element modelling.

    PubMed

    Wang, Xiaofei; Neely, Andrew J; McIlwaine, Gawn G; Lueck, Christian J

    2014-07-18

    The precise mechanism of bitemporal hemianopia (a type of partial visual field defect) is still not clear. Previous work has investigated this problem by studying the biomechanics of chiasmal compression caused by a pituitary tumour growing up from below the optic chiasm. A multi-scale analysis was performed using finite element models to examine both the macro-scale behaviour of the chiasm and the micro-scale interactions of the nerve fibres within it using representative volume elements. Possible effects of large deflection and non-linear material properties were incorporated. Strain distributions in the optic chiasm and optic nerve fibres were obtained from these models. The results of the chiasmal model agreed well with the limited experimental results available, indicating that the finite element modelling can be a useful tool for analysing chiasmal compression. Simulation results showed that the strain distribution in nasal (crossed) nerve fibres was much more nonuniform and locally higher than in temporal (uncrossed) nerve fibres. This strain difference between nasal and temporal nerve fibres may account for the phenomenon of bitemporal hemianopia.

  6. Understanding electrical conduction in lithium ion batteries through multi-scale modeling

    NASA Astrophysics Data System (ADS)

    Pan, Jie

    Silicon (Si) has been considered as a promising negative electrode material for lithium ion batteries (LIBs) because of its high theoretical capacity, low discharge voltage, and low cost. However, the utilization of Si electrode has been hampered by problems such as slow ionic transport, large stress/strain generation, and unstable solid electrolyte interphase (SEI). These problems severely influence the performance and cycle life of Si electrodes. In general, ionic conduction determines the rate performance of the electrode, while electron leakage through the SEI causes electrolyte decomposition and, thus, causes capacity loss. The goal of this thesis research is to design Si electrodes with high current efficiency and durability through a fundamental understanding of the ionic and electronic conduction in Si and its SEI. Multi-scale physical and chemical processes occur in the electrode during charging and discharging. This thesis, thus, focuses on multi-scale modeling, including developing new methods, to help understand these coupled physical and chemical processes. For example, we developed a new method based on ab initio molecular dynamics to study the effects of stress/strain on Li ion transport in amorphous lithiated Si electrodes. This method not only quantitatively shows the effect of stress on ionic transport in amorphous materials, but also uncovers the underlying atomistic mechanisms. However, the origin of ionic conduction in the inorganic components in SEI is different from that in the amorphous Si electrode. To tackle this problem, we developed a model by separating the problem into two scales: 1) atomistic scale: defect physics and transport in individual SEI components with consideration of the environment, e.g., LiF in equilibrium with Si electrode; 2) mesoscopic scale: defect distribution near the heterogeneous interface based on a space charge model. In addition, to help design better artificial SEI, we further demonstrated a theoretical design

  7. A Model of the Saturation of Multi-scale Turbulence by Zonal Flow Mixing

    NASA Astrophysics Data System (ADS)

    Staebler, G. M.; Candy, J.; Holland, C.; Howard, N.

    2016-10-01

    Analysis of the spectrum of the saturated electric potential fluctuations from multi-scale (both ion and electron scales) gyrokinetic turbulence simulations, in tokamak geometry, reveals that fluctuating zonal (axisymmetric) ExB flows couple the ion and electron scales. The zonal flows are driven by the ion-scale instabilities but strongly regulate the amplitude of the electron-scale turbulence. The electron-scale turbulence can grow to large amplitude when the linear growth rate of the ETG modes exceeds the zonal flow mixing rate due to advection of the ETG modes. The model of the zonal flow mixing is shown to capture the suppression of electron-scale turbulence by ion-scale turbulence and the threshold for the increase in electron-scale turbulence when the ion-scale turbulence is reduced. The nonlinear upshift of the effective critical ion temperature gradient (Dimits shift) is also captured by the new model. Prediction of the core plasma fusion performance of ITER with TGLF using the new saturation model yields a 19% increase in fusion power for hybrid regime operation. This work was supported by the US Department of Energy contracts: DE-FG02-95ER54309, DE-FC02-04ER54698, DE-FC02-08ER54963, DE-AC02-05CH11231, DE-FC02-04ER54698, and DE-SC0006957.

  8. Multi-scale modelling of cancer cell intravasation: the role of cadherins in metastasis

    NASA Astrophysics Data System (ADS)

    Ramis-Conde, Ignacio; Chaplain, Mark A. J.; Anderson, Alexander R. A.; Drasdo, Dirk

    2009-03-01

    Transendothelial migration is a crucial process of the metastatic cascade in which a malignant cell attaches itself to the endothelial layer forming the inner wall of a blood or lymph vessel and creates a gap through which it enters into the bloodstream (or lymphatic system) and then is transported to distant parts of the body. In this process both biological pathways involving cell adhesion molecules such as VE-cadherin and N-cadherin, and the biophysical properties of the cells play an important role. In this paper, we present one of the first mathematical models considering the problem of cancer cell intravasation. We use an individual force-based multi-scale approach which accounts for intra- and inter-cellular protein pathways and for the physical properties of the cells, and a modelling framework which accounts for the biological shape of the vessel. Using our model, we study the influence of different protein pathways in the achievement of transendothelial migration and give quantitative simulation results comparable with real experiments.

  9. A multi-scale model for geared transmission aero-thermodynamics

    NASA Astrophysics Data System (ADS)

    McIntyre, Sean M.

    -steady cyclic-symmetric simulation of the internal flow. This high-frequency conduction solution is coupled directly with a model for the meshing friction, developed by a collaborator, which was adapted for use in a finite-volume CFD code. The local surface heat flux on solid surfaces is calculated by time-averaging the heat flux in the high-frequency analysis. This serves as a fixed-flux boundary condition in the long time scale conduction module. The temperature distribution from this long time scale heat transfer calculation serves as a boundary condition for the internal convection simulation, and as the initial condition for the high-frequency heat transfer module. Using this multi-scale model, simulations were performed for equilibrium and loss-of-lubrication operation of the NASA Glenn Research Center test stand. Results were compared with experimental measurements. In addition to the multi-scale model itself, several other specific contributions were made. Eulerian models for droplets and wall-films were developed and im- plemented in the CFD code. A novel approach to retaining liquid film on the solid surfaces, and strategies for its mass exchange with droplets, were developed and verified. Models for interfacial transfer between droplets and wall-film were implemented, and include the effects of droplet deposition, splashing, bouncing, as well as film breakup. These models were validated against airfoil data. To mitigate the observed slow convergence of CFD simulations of the enclosed aerodynamic flows within gearboxes, Fourier stability analysis was applied to the SIMPLE-C fractional-step algorithm. From this, recommendations to accelerate the convergence rate through enhanced pressure-velocity coupling were made. These were shown to be effective. A fast-running finite-volume reduced-order-model of the gearbox aero-thermo- dynamics was developed, and coupled with the tribology model to investigate the sensitivity of loss-of-lubrication predictions to various model

  10. A Multi-scale Modeling System: Developments, Applications and Critical Issues

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo; Chern, Jiundar; Atlas, Robert; Randall, David; Lin, Xin; Khairoutdinov, Marat; Li, Jui-Lin; Waliser, Duane E.; Hou, Arthur; Peters-Lidard, Christa; Lau, William; Simpson, Joanne

    2006-01-01

    A multi-scale modeling framework (MMF), which replaces the conventional cloud parameterizations with a cloud-resolving model (CRM) in each grid column of a GCM, constitutes a new and promising approach. The MMF can provide for global coverage and two-way interactions between the CRMs and their parent GCM. The GCM allows global coverage and the CRM allows explicit simulation of cloud processes and their interactions with radiation and surface processes. A new MMF has been developed that is based the Goddard finite volume GCM (fvGCM) and the Goddard Cumulus Ensemble (GCE) model. This Goddard MMF produces many features that are similar to another MMF that was developed at Colorado State University (CSU), such as an improved .surface precipitation pattern, better cloudiness, improved diurnal variability over both oceans and continents, and a stronger, propagating Madden-Julian oscillation (MJO) compared to their parent GCMs using conventional cloud parameterizations. Both MMFs also produce a precipitation bias in the western Pacific during Northern Hemisphere summer. However, there are also notable differences between two MMFs. For example, the CSU MMF simulates less rainfall over land than its parent GCM. This is why the CSU MMF simulated less overall global rainfall than its parent GCM. The Goddard MMF overestimates global rainfall because of its oceanic component. Some critical issues associated with the Goddard MMF are presented in this paper.

  11. Multi-scale models of grassland passerine abundance in a fragmented system in Wisconsin

    USGS Publications Warehouse

    Renfrew, R.B.; Ribic, C.A.

    2008-01-01

    Fragmentation of grasslands has been implicated in grassland bird population declines. Multi-scale models are being increasingly used to assess potential factors that influence grassland bird presence, abundance, and productivity. However, studies rarely assess fragmentation metrics, and seldom evaluate more than two scales or interactions among scales. We evaluated the relative importance of characteristics at multiple scales to patterns in relative abundance of Savannah Sparrow (Passerculus sandwichensis), Grasshopper Sparrow (Ammodramus savannarum), Eastern Meadowlark (Sturnella magna), and Bobolink (Dolichonyx oryzivorus). We surveyed birds in 74 southwestern Wisconsin pastures from 1997 to 1999 and compared models with explanatory variables from multiple scales: within-patch vegetation structure (microhabitat), patch (macrohabitat), and three landscape extents. We also examined interactions between macrohabitat and landscape factors. Core area of pastures was an important predictor of relative abundance, and composition of the landscape was more important than configuration. Relative abundance was frequently higher in pastures with more core area and in landscapes with more grassland and less wooded area. The direction and strength of the effect of core pasture size on relative abundance changed depending on amount of wooded area in the landscape. Relative abundance of grassland birds was associated with landscape variables more frequently at the 1200-m scale than at smaller scales. To develop better predictive models, parameters at multiple scales and their interactive effects should be included, and results should be evaluated in the context of microhabitat variability, landscape composition, and fragmentation in the study area. ?? 2007 Springer Science+Business Media B.V.

  12. Advanced Integration in Multi-Scale Mechanics and Welding Process Simulation in Weld Integrity Assessment

    SciTech Connect

    Vitek, J.M.; Wilkowski, G.M.; Brust, F.W.; Babu, S.

    2008-01-30

    In this project, mathematical models that predict the microstructure in pipeline steel welds were to be developed. These models were to be integrated with thermal models that describe the time-temperature history in the weld as a function of location in order to derive the spatial variation of microstructure in the weld. The microstructure predictions were also to be combined with microstructure-hardness relations, based on the additivity principle, to determine the spatial variation of hardness in the weld. EMC2 also developed microstructural models based on empirical relationships. ORNL was to pursue the development of more fundamental, theoretically based models. ORNL applied a previously developed model for inclusion formation to predict the extent and nature of inclusions that form during weld cooling from the liquid. This inclusion model was directly integrated with computational thermodynamics capability. A convenient user interface was developed for both the inclusion model and the thermodynamic phase-stability calculations. The microstructure model was based on the simultaneous transformation theory analysis as applied to the transformation of austenite to various ferrite constituents during weld cooling. The model available on the Materials Algorithm Project web site was used. Extensive modification of this model was required to correct problems with compilation and calculations as a function of the computational platform (Unix, Linux, Windows, etc.) that was used. The user interface for the inclusion model and thermodynamic phase-stability calculations was delivered to EMC2 along with the modified and correct microstructure model. Evaluation of the theoretically based model will be carried out and the predictions will be compared with experimental results as well as predictions based on the empirical models developed by EMC2.

  13. Realistic Modeling of Multi-Scale MHD Dynamics of the Solar Atmosphere

    NASA Technical Reports Server (NTRS)

    Kitiashvili, Irina; Mansour, Nagi N.; Wray, Alan; Couvidat, Sebastian; Yoon, Seokkwan; Kosovichev, Alexander

    2014-01-01

    Realistic 3D radiative MHD simulations open new perspectives for understanding the turbulent dynamics of the solar surface, its coupling to the atmosphere, and the physical mechanisms of generation and transport of non-thermal energy. Traditionally, plasma eruptions and wave phenomena in the solar atmosphere are modeled by prescribing artificial driving mechanisms using magnetic or gas pressure forces that might arise from magnetic field emergence or reconnection instabilities. In contrast, our 'ab initio' simulations provide a realistic description of solar dynamics naturally driven by solar energy flow. By simulating the upper convection zone and the solar atmosphere, we can investigate in detail the physical processes of turbulent magnetoconvection, generation and amplification of magnetic fields, excitation of MHD waves, and plasma eruptions. We present recent simulation results of the multi-scale dynamics of quiet-Sun regions, and energetic effects in the atmosphere and compare with observations. For the comparisons we calculate synthetic spectro-polarimetric data to model observational data of SDO, Hinode, and New Solar Telescope.

  14. Multi-scale needle-network model of complex dendritic microstructure formation

    NASA Astrophysics Data System (ADS)

    Tourret, Damien; Karma, Alain

    2012-07-01

    We present a novel multi-scale Dendritic Needle Network (DNN) approach in order to model well-developed highly-ramified dendritic microstructures on the coarser scale of several crystal grains while retaining a faithful quantitative description of the transient dynamics of individual dendritic branches. This approach is intended to bridge the scale gap between phase-field and cellular automaton methods. The dynamics of each needle-like branch, characterized by its tip velocity V and radius ρ, is fixed by two conditions: (i) on the inner tip scale, a standard microscopic solvability condition relates ρ2V to the strength of surface tension anisotropy, and (ii) on the outer diffusion length scale, a flux balance condition relates the product ρV2 to a flux intensity factor extracted from a contour integral analogous to the J-integral of fracture mechanics. The method is tested for low supersaturation and reproduces the analytical solutions for both early stage and steady state growth dynamics. The results are directly compared with a quantitative phase-field simulation for an experimentally relevant supersaturation. We present as well an illustrative simulation for highly branched polycrystalline growth. This model should permit to investigate the macroscale grain evolution through the dynamics of individual primary dendrites and higher-order branches, controlled by both the intragrain history-dependent selection and the intergrain dendrite interactions.

  15. Global Climate Simulation in a Multi-scale Modeling Framework: Sensitivity to GCM- Resolution

    NASA Astrophysics Data System (ADS)

    Duffy, P. B.; Bala, G.; Gleckler, P. J.; Taylor, K. E.; Mirin, A. A.; Wickett, M. E.

    2006-12-01

    We investigate sensitivity of the simulated climate in the NCAR CAM3 atmospheric climate model to increases in horizontal spatial resolution, and to use an alternative representation of unresolved motions. In the Multi-scale Modeling Framework (MMF), cloud parameterizations in are replaced by a two-dimensional Cloud System Resolving Model (CSRM) that is embedded in each column of the general circulation model (GCM. Here we investigate both the resolution-sensitivity of the baseline version (that employing parameterizations) of the CAM3 atmospheric model as well as the sensitivity to decreasing the horizontal grid size of the GCM in an MMF version of the same model. Generally speaking, climate quantities related to clouds, precipitation, and radiative fluxes are more sensitive to treatment of subgrid scale processes than to GCM grid size. Simulated top-of-atmosphere cloud radiative forcings and related radiative fluxes are substantially improved in the MMF simulations; aspects of simulated precipitation and the simulated MJO are also substantially improved. In both the MMF and parameterized simulations, the large-scale climate shows less sensitivity to GCM resolution than has been seen in some other models, particularly the NCAR CCM3, a predecessor to CAM3. However, comparison to published simulations using CAM3 with Eulerian spectral dynamics indicates that that CAM3 configuration has very similar sensitivities to horizontal resolution as the Finite Volume dynamics version used here; comparison to MMF simulations with different GCM grid sizes confirms that parameterized physics influences resolution-sensitivity more than dynamical formulation does. Because the MMF is based more closely on first-principles physics than parameterizations are, one need not retune model parameters when the horizontal resolution of the GCM is changed in the MMF.

  16. A multi-scale computational model of the effects of TMS on motor cortex

    PubMed Central

    Seo, Hyeon; Schaworonkow, Natalie; Jun, Sung Chan; Triesch, Jochen

    2017-01-01

    The detailed biophysical mechanisms through which transcranial magnetic stimulation (TMS) activates cortical circuits are still not fully understood. Here we present a multi-scale computational model to describe and explain the activation of different pyramidal cell types in motor cortex due to TMS. Our model determines precise electric fields based on an individual head model derived from magnetic resonance imaging and calculates how these electric fields activate morphologically detailed models of different neuron types. We predict neural activation patterns for different coil orientations consistent with experimental findings. Beyond this, our model allows us to calculate activation thresholds for individual neurons and precise initiation sites of individual action potentials on the neurons’ complex morphologies. Specifically, our model predicts that cortical layer 3 pyramidal neurons are generally easier to stimulate than layer 5 pyramidal neurons, thereby explaining the lower stimulation thresholds observed for I-waves compared to D-waves. It also shows differences in the regions of activated cortical layer 5 and layer 3 pyramidal cells depending on coil orientation. Finally, it predicts that under standard stimulation conditions, action potentials are mostly generated at the axon initial segment of cortical pyramidal cells, with a much less important activation site being the part of a layer 5 pyramidal cell axon where it crosses the boundary between grey matter and white matter. In conclusion, our computational model offers a detailed account of the mechanisms through which TMS activates different cortical pyramidal cell types, paving the way for more targeted application of TMS based on individual brain morphology in clinical and basic research settings.

  17. Multi-scale modelling of strongly heterogeneous 3D composite structures using spatial Voronoi tessellation

    NASA Astrophysics Data System (ADS)

    El Said, Bassam; Ivanov, Dmitry; Long, Andrew C.; Hallett, Stephen R.

    2016-03-01

    3D composite materials are characterized by complex internal yarn architectures, leading to complex deformation and failure development mechanisms. Net-shaped preforms, which are originally periodic in nature, lose their periodicity when the fabric is draped, deformed on a tool, and consolidated to create geometrically complex composite components. As a result, the internal yarn architecture, which dominates the mechanical behaviour, becomes dependent on the structural geometry. Hence, predicting the mechanical behaviour of 3D composites requires an accurate representation of the yarn architecture within structural scale models. When applied to 3D composites, conventional finite element modelling techniques are limited to either homogenised properties at the structural scale, or the unit cell scale for a more detailed material property definition. Consequently, these models fail to capture the complex phenomena occurring across multiple length scales and their effects on a 3D composite's mechanical response. Here a multi-scale modelling approach based on a 3D spatial Voronoi tessellation is proposed. The model creates an intermediate length scale suitable for homogenisation to deal with the non-periodic nature of the final material. Information is passed between the different length scales to allow for the effect of the structural geometry to be taken into account on the smaller scales. The stiffness and surface strain predictions from the proposed model have been found to be in good agreement with experimental results. The proposed modelling framework has been used to gain important insight into the behaviour of this category of materials. It has been observed that the strain and stress distributions are strongly dependent on the internal yarn architecture and consequently on the final component geometry. Even for simple coupon tests, the internal architecture and geometric effects dominate the mechanical response. Consequently, the behaviour of 3D woven

  18. Predictive Maturity of Multi-Scale Simulation Models for Fuel Performance

    SciTech Connect

    Atamturktur, Sez; Unal, Cetin; Hemez, Francois; Williams, Brian; Tome, Carlos

    2015-03-16

    The project proposed to provide a Predictive Maturity Framework with its companion metrics that (1) introduce a formalized, quantitative means to communicate information between interested parties, (2) provide scientifically dependable means to claim completion of Validation and Uncertainty Quantification (VU) activities, and (3) guide the decision makers in the allocation of Nuclear Energy’s resources for code development and physical experiments. The project team proposed to develop this framework based on two complimentary criteria: (1) the extent of experimental evidence available for the calibration of simulation models and (2) the sophistication of the physics incorporated in simulation models. The proposed framework is capable of quantifying the interaction between the required number of physical experiments and degree of physics sophistication. The project team has developed this framework and implemented it with a multi-scale model for simulating creep of a core reactor cladding. The multi-scale model is composed of the viscoplastic self-consistent (VPSC) code at the meso-scale, which represents the visco-plastic behavior and changing properties of a highly anisotropic material and a Finite Element (FE) code at the macro-scale to represent the elastic behavior and apply the loading. The framework developed takes advantage of the transparency provided by partitioned analysis, where independent constituent codes are coupled in an iterative manner. This transparency allows model developers to better understand and remedy the source of biases and uncertainties, whether they stem from the constituents or the coupling interface by exploiting separate-effect experiments conducted within the constituent domain and integral-effect experiments conducted within the full-system domain. The project team has implemented this procedure with the multi- scale VPSC-FE model and demonstrated its ability to improve the predictive capability of the model. Within this

  19. HYPERstream: a multi-scale framework for streamflow routing in large-scale hydrological model

    NASA Astrophysics Data System (ADS)

    Piccolroaz, Sebastiano; Di Lazzaro, Michele; Zarlenga, Antonio; Majone, Bruno; Bellin, Alberto; Fiori, Aldo

    2016-05-01

    We present HYPERstream, an innovative streamflow routing scheme based on the width function instantaneous unit hydrograph (WFIUH) theory, which is specifically designed to facilitate coupling with weather forecasting and climate models. The proposed routing scheme preserves geomorphological dispersion of the river network when dealing with horizontal hydrological fluxes, irrespective of the computational grid size inherited from the overlaying climate model providing the meteorological forcing. This is achieved by simulating routing within the river network through suitable transfer functions obtained by applying the WFIUH theory to the desired level of detail. The underlying principle is similar to the block-effective dispersion employed in groundwater hydrology, with the transfer functions used to represent the effect on streamflow of morphological heterogeneity at scales smaller than the computational grid. Transfer functions are constructed for each grid cell with respect to the nodes of the network where streamflow is simulated, by taking advantage of the detailed morphological information contained in the digital elevation model (DEM) of the zone of interest. These characteristics make HYPERstream well suited for multi-scale applications, ranging from catchment up to continental scale, and to investigate extreme events (e.g., floods) that require an accurate description of routing through the river network. The routing scheme enjoys parsimony in the adopted parametrization and computational efficiency, leading to a dramatic reduction of the computational effort with respect to full-gridded models at comparable level of accuracy. HYPERstream is designed with a simple and flexible modular structure that allows for the selection of any rainfall-runoff model to be coupled with the routing scheme and the choice of different hillslope processes to be represented, and it makes the framework particularly suitable to massive parallelization, customization according to

  20. Simulations of ecosystem hydrological processes using a unified multi-scale model

    SciTech Connect

    Yang, Xiaofan; Liu, Chongxuan; Fang, Yilin; Hinkle, Ross; Li, Hong-Yi; Bailey, Vanessa; Bond-Lamberty, Ben

    2015-01-01

    This paper presents a unified multi-scale model (UMSM) that we developed to simulate hydrological processes in an ecosystem containing both surface water and groundwater. The UMSM approach modifies the Navier–Stokes equation by adding a Darcy force term to formulate a single set of equations to describe fluid momentum and uses a generalized equation to describe fluid mass balance. The advantage of the approach is that the single set of the equations can describe hydrological processes in both surface water and groundwater where different models are traditionally required to simulate fluid flow. This feature of the UMSM significantly facilitates modelling of hydrological processes in ecosystems, especially at locations where soil/sediment may be frequently inundated and drained in response to precipitation, regional hydrological and climate changes. In this paper, the UMSM was benchmarked using WASH123D, a model commonly used for simulating coupled surface water and groundwater flow. Disney Wilderness Preserve (DWP) site at the Kissimmee, Florida, where active field monitoring and measurements are ongoing to understand hydrological and biogeochemical processes, was then used as an example to illustrate the UMSM modelling approach. The simulations results demonstrated that the DWP site is subject to the frequent changes in soil saturation, the geometry and volume of surface water bodies, and groundwater and surface water exchange. All the hydrological phenomena in surface water and groundwater components including inundation and draining, river bank flow, groundwater table change, soil saturation, hydrological interactions between groundwater and surface water, and the migration of surface water and groundwater interfaces can be simultaneously simulated using the UMSM. Overall, the UMSM offers a cross-scale approach that is particularly suitable to simulate coupled surface and ground water flow in ecosystems with strong surface water and groundwater interactions.

  1. Multi-Scale Model of Galactic Cosmic Ray Effects on the Hippocampus

    NASA Astrophysics Data System (ADS)

    Cucinotta, Francis

    An important concern for risk assessment from galactic cosmic ray (GCR) exposures is impacts to the central nervous systems including changes in cognition, and associations with increased risk of Alzheimer’s disease (AD). AD, which affects about 50 percent of the population above age 80-yr, is a degenerative disease that worsens with time after initial onset leading to death, and has no known cure. AD is difficult to detect at early stages, and the small number of epidemiology studies that have considered the possibility have not identified an association with low dose radiation. However, experimental studies in transgenic mice suggest the possibility exits. We discuss modeling approaches to consider mechanisms whereby GCR would accelerate the occurrence of AD to earlier ages. Biomarkers of AD include Amyloid beta plaques, and neurofibrillary tangles (NFT) made up of aggregates of the hyper-phosphorylated form of the micro-tubule associated, tau protein. Related markers include synaptic degeneration, dendritic spine loss, and neuronal cell loss through apoptosis. GCR may affect these processes by causing oxidative stress, aberrant signaling following DNA damage, and chronic neuro-inflammation. Cell types considered in multi-scale models are neurons, astrocytes, and microglia. We developed biochemical and cell kinetics models of DNA damage signaling related to glycogen synthase kinase-3 beta and neuro-inflammation, and considered approaches to develop computer simulations of GCR induced cell interactions and their relationships to Amyloid beta plaques and NFTs. Comparison of model results to experimental data for the age specific development of plaques in transgenic mice and predictions of space radiation effects will be discussed.

  2. Cloud-resolving component in the quasi-3D multi-scale modeling framework

    NASA Astrophysics Data System (ADS)

    Jung, Joon-Hee; Arakawa, Akio

    2010-05-01

    A quasi-3D multi-scale modeling framework (Q3D MMF), which combines a GCM with a Q3D CRM, is an attempt to include three dimensional cloud effects in a GCM without necessarily using a global cloud-resolving model. The horizontal domain of the Q3D CRM consists of two perpendicular sets of channels crossing at the center of a GCM grid box, each of which includes two grid-point arrays. Through coupling this structure with a GCM, the whole system of the Q3D MMF can converge to a fully 3D global CRM as the GCM's resolution is refined. Consequently, the horizontal resolution of the GCM can be freely chosen depending on the objective of application. However, due to the use of very narrow channels for the cloud-resolving component, its prediction algorithm must be specially designed. As a step in developing a Q3D MMF, we have first constructed a prediction algorithm for the Q3D CRM applying a 3D anelastic vector vorticity equation model to the Q3D network of grid points. Preliminary tests of the Q3D CRM have been performed for an idealized small domain. Comparing the results with those of the straightforward application of a 3D CRM, it is concluded that the Q3D CRM can reproduce most of the important statistics of the 3D solutions and the MMF based on the Q3D CRM will be a useful framework for climate modeling. This paper presents an outline of the Q3D algorithm and highlights of the results.

  3. Object-based class modelling for multi-scale riparian forest habitat mapping

    NASA Astrophysics Data System (ADS)

    Strasser, Thomas; Lang, Stefan

    2015-05-01

    Object-based class modelling allows for mapping complex, hierarchical habitat systems. The riparian zone, including forests, represents such a complex ecosystem. Forests within riparian zones are biologically high productive and characterized by a rich biodiversity; thus considered of high community interest with an imperative to be protected and regularly monitored. Satellite earth observation (EO) provides tools for capturing the current state of forest habitats such as forest composition including intermixture of non-native tree species. Here we present a semi-automated object based image analysis (OBIA) approach for the mapping of riparian forests by applying class modelling of habitats based on the European Nature Information System (EUNIS) habitat classifications and the European Habitats Directive (HabDir) Annex 1. A very high resolution (VHR) WorldView-2 satellite image provided the required spatial and spectral details for a multi-scale image segmentation and rule-base composition to generate a six-level hierarchical representation of riparian forest habitats. Thereby habitats were hierarchically represented within an image object hierarchy as forest stands, stands of homogenous tree species and single trees represented by sunlit tree crowns. 522 EUNIS level 3 (EUNIS-3) habitat patches with a mean patch size (MPS) of 12,349.64 m2 were modelled from 938 forest stand patches (MPS = 6868.20 m2) and 43,742 tree stand patches (MPS = 140.79 m2). The delineation quality of the modelled EUNIS-3 habitats (focal level) was quantitatively assessed to an expert-based visual interpretation showing a mean deviation of 11.71%.

  4. Towards an integrated and multi-scale model of the land-sea continuum

    NASA Astrophysics Data System (ADS)

    De Maet, T.; Hanert, E.

    2012-04-01

    The land-sea continuum is home to a rich and complex system, controlled by strong exchanges of material and energy between land, sea and atmosphere. All the elements of such a system have to be taken into account to understand the whole process, which means explicitly linking together the watersheds, rivers, estuaries and coastal seas. A central issue is that the involved processes take place at very different scales in space and time. To overcome this issue, we consider an integrated model using a multi-scale framework, based on the finite element method (FEM) and unstructured meshes. In this presentation we focus on surface and subsurface models which are both fully-explicit for optimal scaling on parallel architectures. These models have been coupled with the hydrodynamical model SLIM1 which is currently able to model the river-estuary-coastal sea continuum. All these models use the discontinuous Galerkin (DG) FEM and include a tracer transport module. The 3D variably saturated groundwater model is based on the Richards equation, the 2D surface water model uses the diffusive wave approximation of the shallow water equation and the 1D river model is based on the full shallow water equation. As the overall model is designed for large scale simulations, we assume that small rivers are included in the surface model. Explicit methods in time allow for perfect parallel scaling and easy coupling. Our explicit model for the saturated-unsaturated subsurface water is robust and fully conservative. It is based on a mixed formulation, using both the pressure head h and the water content θ. On the one hand, θ is used for the unsaturated zone, where it is know to be more efficient. On the other hand h is used for the saturated zone, where θ is constant. To produce an explicit formulation of the Richards equation, we use the false transient method in the saturated zone, where the hydrodynamics is described by an elliptic equation. To allow physical discontinuities between

  5. Multi-scale modeling of fiber and fabric reinforced cement based composites

    NASA Astrophysics Data System (ADS)

    Soranakom, Chote

    With an increased use of fiber reinforced concrete in structural applications, proper characterization techniques and development of design guides are needed. This dissertation presents a multi-scale modeling approach for fiber and fabric reinforced cement-based composites. A micromechanics-based model of the yarn pullout mechanism due to the failure of the interfacial zone is presented. The effect of mechanical anchorage of transverse yarns is simulated using nonlinear spring elements. The yarn pullout mechanism was used in a meso-scale modeling approach to simulate the yarn bridging force in the crack evolution process. The tensile stress-strain response of a tension specimen that experiences distributed cracking can be simulated using a generalized finite difference approach. The stiffness degradation, tension stiffening, crack spacing evolution, and crack width characteristics of cement composites can be derived using matrix, interface and fiber properties. The theoretical models developed for fabric reinforced cement composites were then extended to cover other types of fiber reinforced concrete such as shotcrete, glass fiber reinforced concrete (GFRC), steel fiber reinforced concrete (SFRC), ferrocement and other conventional composite systems. The uniaxial tensile stress-strain response was used to formulate a generalized parametric closed-form solution for predicting flexural behavior of various composites at the macro-structural level. The flexural behaviors of these composites were modeled in a unified manner by means of a moment-curvature relationship based on the uniaxial material models. A variety of theoretical models were developed to address the various mechanisms including: an analytical yarn pullout model; a nonlinear finite difference fabric pullout model; a nonlinear finite difference tension model; closed-form solutions for strain-softening materials; closed-form solutions for strain-softening/hardening materials; and closed-form solutions for

  6. A Nonlinear Multi-Scale Interaction Model for Atmospheric Blocking: The Eddy-Blocking Matching Mechanism

    NASA Astrophysics Data System (ADS)

    Luo, Dehai; Cha, Jing; Zhong, Linhao; Dai, Aiguo

    2014-05-01

    In this paper, a nonlinear multi-scale interaction (NMI) model is used to propose an eddy-blocking matching (EBM) mechanism to account for how synoptic eddies reinforce or suppress a blocking flow. It is shown that the spatial structure of the eddy vorticity forcing (EVF) arising from upstream synoptic eddies determines whether an incipient block can grow into a meandering blocking flow through its interaction with the transient synoptic eddies from the west. Under certain conditions, the EVF exhibits a low-frequency oscillation on timescales of 2-3 weeks. During the EVF phase with a negative-over- positive dipole structure, a blocking event can be resonantly excited through the transport of eddy energy into the incipient block by the EVF. As the EVF changes into an opposite phase, the blocking decays. The NMI model produces life cycles of blocking events that resemble observations. Moreover, it is shown that the eddy north-south straining is a response of the eddies to a dipole- or Ω-type block. In our model, as in observations, two synoptic anticyclones (cyclones) can attract and merge with one another as the blocking intensifies, but only when the feedback of the blocking on the eddies is included. Thus, we attribute the eddy straining and associated vortex interaction to the feedback of the intensified blocking on synoptic eddies. The results illustrate the concomitant nature of the eddy deformation, whose role as a PV source for the blocking flow becomes important only during the mature stage of a block. Our EBM mechanism suggests that an incipient block flow is amplified (or suppressed) under certain conditions by the EVF coming from the upstream of the blocking region.

  7. The NCEP Eulerian Non-hydrostatic Multi-scale Model (NMMB)

    NASA Astrophysics Data System (ADS)

    Janjic, Zavisa; Vasic, Ratko; Jovic, Dusan; Black, Tom

    2014-05-01

    The development of the unified Non-hydrostatic Multi-scale Model (NMMB) has continued at NCEP. The model dynamics preserve a number of important properties of differential operators and conserve a variety of first order and quadratic quantities. The nonlinear dynamics is controlled by conserving energy and enstrophy in case of non-divergent flow. Over-specification of vertical velocity is avoided. The physical package was developed from the WRF NMM's physics, but other physics options are also available. The regional version of the NMMB is run operationally as the main deterministic North American short-range forecasting model (NAM) and in a number of other applications. The global NMMB also has been run over the last few years experimentally in order to assess its capabilities and develop it further. In terms of large scale metrics, the performance of the global NMMB in medium range weather forecasting has been generally comparable to that of other major medium range forecasting systems. Its computational efficiency satisfies and exceeds the current and projected operational requirements. Recently, the transition has started of the operational hurricane forecasting system HWRF from the WRF NMM dynamics to those of the NMMB. This system involves the use of a hierarchy of 2-way interactive telescoping moving nests. The work on the interaction between clouds and radiation has continued. Extended range forecasts showed large sensitivity to the method for representing clouds. With the clouds represented by optical properties of their microphysics species, the results depend on the microphysics scheme used. Taking into account the impact of convective clouds remains a challenge with this approach. Development of an indigenous data assimilation system for the global NMMB has commenced. The system is based on the hybrid ensemble Kalman filter/3DVAR technique. It is believed that the potential of the NMMB can be better assessed using its own dedicated data assimilation

  8. ADVANCED INTEGRATION OF MULTI-SCALE MECHANICS AND WELDING PROCESS SIMULATION IN WELD INTEGRITY ASSESSMENT

    SciTech Connect

    Wilkowski, Gery M.; Rudland, David L.; Shim, Do-Jun; Brust, Frederick W.; Babu, Sundarsanam

    2008-06-30

    The potential to save trillions of BTU’s in energy usage and billions of dollars in cost on an annual basis based on use of higher strength steel in major oil and gas transmission pipeline construction is a compelling opportunity recognized by both the US Department of Energy (DOE). The use of high-strength steels (X100) is expected to result in energy savings across the spectrum, from manufacturing the pipe to transportation and fabrication, including welding of line pipe. Elementary examples of energy savings include more the 25 trillion BTUs saved annually based on lower energy costs to produce the thinner-walled high-strength steel pipe, with the potential for the US part of the Alaskan pipeline alone saving more than 7 trillion BTU in production and much more in transportation and assembling. Annual production, maintenance and installation of just US domestic transmission pipeline is likely to save 5 to 10 times this amount based on current planned and anticipated expansions of oil and gas lines in North America. Among the most important conclusions from these studies were: • While computational weld models to predict residual stress and distortions are well-established and accurate, related microstructure models need improvement. • Fracture Initiation Transition Temperature (FITT) Master Curve properly predicts surface-cracked pipe brittle-to-ductile initiation temperature. It has value in developing Codes and Standards to better correlate full-scale behavior from either CTOD or Charpy test results with the proper temperature shifts from the FITT master curve method. • For stress-based flaw evaluation criteria, the new circumferentially cracked pipe limit-load solution in the 2007 API 1104 Appendix A approach is overly conservative by a factor of 4/π, which has additional implications. . • For strain-based design of girth weld defects, the hoop stress effect is the most significant parameter impacting CTOD-driving force and can increase the crack

  9. A switching multi-scale dynamical network model of EEG/MEG.

    PubMed

    Olier, Iván; Trujillo-Barreto, Nelson J; El-Deredy, Wael

    2013-12-01

    We introduce a new generative model of the Encephalography (EEG/MEG) data, the inversion of which allows for inferring the locations and temporal evolution of the underlying sources as well as their dynamical interactions. The proposed Switching Mesostate Space Model (SMSM) builds on the multi-scale generative model for EEG/MEG by Daunizeau and Friston (2007). SMSM inherits the assumptions that (1) bioelectromagnetic activity is generated by a set of distributed sources, (2) the dynamics of these sources can be modelled as random fluctuations about a small number of mesostates, and (3) the number of mesostates engaged by a cognitive task is small. Additionally, four generalising assumptions are now included: (4) the mesostates interact according to a full Dynamical Causal Network (DCN) that can be estimated; (5) the dynamics of the mesostates can switch between multiple approximately linear operating regimes; (6) each operating regime remains stable over finite periods of time (temporal clusters); and (7) the total number of times the mesostates' dynamics can switch is small. The proposed model adds, therefore, a level of flexibility by accommodating complex brain processes that cannot be characterised by purely linear and stationary Gaussian dynamics. Importantly, the SMSM furnishes a new interpretation of the EEG/MEG data in which the source activity may have multiple discrete modes of behaviour, each with approximately linear dynamics. This is modelled by assuming that the connection strengths of the underlying mesoscopic DCN are time-dependent but piecewise constant, i.e. they can undergo discrete changes over time. A Variational Bayes inversion scheme is derived to estimate all the parameters of the model by maximising a (Negative Free Energy) lower bound on the model evidence. This bound is used to select among different model choices that are defined by the number of mesostates as well as by the number of stationary linear regimes. The full model is compared

  10. Multi-scale modeling of the structure and dynamics of macromolecules

    NASA Astrophysics Data System (ADS)

    Serohijos, Adrian Wendil R.

    Biology is defined by phenomena that are inherently complex spanning multiple length and time scales. To understand these processes, there is a need for multi-scale approaches that provide a coherent framework for describing and interrogating these phenomena. Here, we employ multiple approaches to investigate specific biological systems. The first system we studied was the cytoplasmic dynein motor, a protein that walks along the microtubule tracks in cells. The major objective in the dynein motors field is to understand its mechanism. Specifically, what is dynein's structure and how does it transduce chemical energy into mechanical work? We proposed a theoretical structural model of the motor and performed normal mode analysis and molecular dynamics on the motor unit structure. These studies hypothesized new structural features in the dynein motor unit and proposed a potential mechanism for energy transduction [5,6,80]. The second system we studied was the CFTR channel, which regulates ion transport in the apical membrane of epithelial cells. Mutations in the CFTR protein are the basis of the cystic fibosis disease. One of the primary question is how a single residue deletion (Phe508) lead to ˜90% of cystic fibrosis cases. We performed molecular dynamics simulation of the first nucleotide-binding domain of CFTR and showed that the wild type and mutant exhibit a difference in their folding kinetics, in agreement with experiments. These simulations also determined the potential structural origin of this misfolding defect. We also proposed a complete model of the CFTR channel to identify the location of the Phe508 residue in the whole protein. This result is important in understanding another aspect of the DeltaF508 defect, which is the misassembly of the whole CFTR protein during its biosynthesis.

  11. A multi-scale biomechanical model based on the physiological structure and lignocellulose components of wheat straw.

    PubMed

    Chen, Longjian; Li, Aiwei; He, Xueqin; Han, Lujia

    2015-11-20

    Biomechanical behavior is a fundamental property for the efficient utilization of wheat straw in such applications as fuel and renewable materials. Tensile experiments and lignocellulose analyses were performed on three types of wheat straw. A multi-scale finite element model composed of the microscopic model of the microfibril equivalent volume element and the macroscopic model of straw tissue was proposed based on the physiological structure and lignocellulose components of wheat straw. The tensile properties of wheat straw were simulated by ANSYS software. The predicted stress-strain data were compared with the observed data, and good correspondence was achieved for all three types of wheat straw. The validated multi-scale finite-element (FE) model was then used to investigate the effect of the lignocellulose components on the biomechanical properties of wheat straw. More than 80% of stress is carried by the cellulose fiber, whereas the strain is mainly carried by the amorphous cellulose.

  12. Ground motions characterized by a multi-scale heterogeneous earthquake model

    NASA Astrophysics Data System (ADS)

    Aochi, Hideo; Ide, Satoshi

    2014-12-01

    We have carried out numerical simulations of seismic ground motion radiating from a mega-earthquake whose rupture process is governed by a multi-scale heterogeneous distribution of fracture energy. The observed complexity of the Mw 9.0 2011 Tohoku-Oki earthquake can be explained by such heterogeneities with fractal patches (size and number), even without introducing any heterogeneity in the stress state. In our model, scale dependency in fracture energy (i.e., the slip-weakening distance D c) on patch size is essential. Our results indicate that wave radiation is generally governed by the largest patch at each moment and that the contribution from small patches is minor. We then conducted parametric studies on the frictional parameters of peak ( τ p) and residual ( τ r) friction to produce the case where the effect of the small patches is evident during the progress of the main rupture. We found that heterogeneity in τ r has a greater influence on the ground motions than does heterogeneity in τ p. As such, local heterogeneity in the static stress drop (Δ τ) influences the rupture process more than that in the stress excess (Δ τ excess). The effect of small patches is particularly evident when these are almost geometrically isolated and not simultaneously involved in the rupture of larger patches. In other cases, the wave radiation from small patches is probably hidden by the major contributions from large patches. Small patches may play a role in strong motion generation areas with low τ r (high Δ τ), particularly during slow average rupture propagation. This effect can be identified from the differences in the spatial distributions of peak ground velocities for different frequency ranges.

  13. Multi-scale Rule-of-Mixtures Model of Carbon Nanotube/Carbon Fiber/Epoxy Lamina

    NASA Technical Reports Server (NTRS)

    Frankland, Sarah-Jane V.; Roddick, Jaret C.; Gates, Thomas S.

    2005-01-01

    A unidirectional carbon fiber/epoxy lamina in which the carbon fibers are coated with single-walled carbon nanotubes is modeled with a multi-scale method, the atomistically informed rule-of-mixtures. This multi-scale model is designed to include the effect of the carbon nanotubes on the constitutive properties of the lamina. It included concepts from the molecular dynamics/equivalent continuum methods, micromechanics, and the strength of materials. Within the model both the nanotube volume fraction and nanotube distribution were varied. It was found that for a lamina with 60% carbon fiber volume fraction, the Young's modulus in the fiber direction varied with changes in the nanotube distribution, from 138.8 to 140 GPa with nanotube volume fractions ranging from 0.0001 to 0.0125. The presence of nanotube near the surface of the carbon fiber is therefore expected to have a small, but positive, effect on the constitutive properties of the lamina.

  14. Simulations of Tornadoes, Tropical Cyclones, MJOs, and QBOs, using GFDL's multi-scale global climate modeling system

    NASA Astrophysics Data System (ADS)

    Lin, Shian-Jiann; Harris, Lucas; Chen, Jan-Huey; Zhao, Ming

    2014-05-01

    A multi-scale High-Resolution Atmosphere Model (HiRAM) is being developed at NOAA/Geophysical Fluid Dynamics Laboratory. The model's dynamical framework is the non-hydrostatic extension of the vertically Lagrangian finite-volume dynamical core (Lin 2004, Monthly Wea. Rev.) constructed on a stretchable (via Schmidt transformation) cubed-sphere grid. Physical parametrizations originally designed for IPCC-type climate predictions are in the process of being modified and made more "scale-aware", in an effort to make the model suitable for multi-scale weather-climate applications, with horizontal resolution ranging from 1 km (near the target high-resolution region) to as low as 400 km (near the antipodal point). One of the main goals of this development is to enable simulation of high impact weather phenomena (such as tornadoes, thunderstorms, category-5 hurricanes) within an IPCC-class climate modeling system previously thought impossible. We will present preliminary results, covering a very wide spectrum of temporal-spatial scales, ranging from simulation of tornado genesis (hours), Madden-Julian Oscillations (intra-seasonal), topical cyclones (seasonal), to Quasi Biennial Oscillations (intra-decadal), using the same global multi-scale modeling system.

  15. Selective ensemble modeling load parameters of ball mill based on multi-scale frequency spectral features and sphere criterion

    NASA Astrophysics Data System (ADS)

    Tang, Jian; Yu, Wen; Chai, Tianyou; Liu, Zhuo; Zhou, Xiaojie

    2016-01-01

    It is difficult to model multi-frequency signal, such as mechanical vibration and acoustic signals of wet ball mill in the mineral grinding process. In this paper, these signals are decomposed into multi-scale intrinsic mode functions (IMFs) by the empirical mode decomposition (EMD) technique. A new adaptive multi-scale spectral features selection approach based on sphere criterion (SC) is applied to these IMFs frequency spectra. The candidate sub-models are constructed by the partial least squares (PLS) with the selected features. Finally, the branch and bound based selective ensemble (BBSEN) algorithm is applied to select and combine these ensemble sub-models. This method can be easily extended to regression and classification problems with multi-time scale signal. We successfully apply this approach to a laboratory-scale ball mill. The shell vibration and acoustic signals are used to model mill load parameters. The experimental results demonstrate that this novel approach is more effective than the other modeling methods based on multi-scale frequency spectral features.

  16. A multi-scale hybrid neural network retrieval model for dust storm detection, a study in Asia

    NASA Astrophysics Data System (ADS)

    Wong, Man Sing; Xiao, Fei; Nichol, Janet; Fung, Jimmy; Kim, Jhoon; Campbell, James; Chan, P. W.

    2015-05-01

    Dust storms are known to have adverse effects on human health and significant impact on weather, air quality, hydrological cycle, and ecosystem. Atmospheric dust loading is also one of the large uncertainties in global climate modeling, due to its significant impact on the radiation budget and atmospheric stability. Observations of dust storms in humid tropical south China (e.g. Hong Kong), are challenging due to high industrial pollution from the nearby Pearl River Delta region. This study develops a method for dust storm detection by combining ground station observations (PM10 concentration, AERONET data), geostationary satellite images (MTSAT), and numerical weather and climatic forecasting products (WRF/Chem). The method is based on a hybrid neural network (NN) retrieval model for two scales: (i) a NN model for near real-time detection of dust storms at broader regional scale; (ii) a NN model for detailed dust storm mapping for Hong Kong and Taiwan. A feed-forward multilayer perceptron (MLP) NN, trained using back propagation (BP) algorithm, was developed and validated by the k-fold cross validation approach. The accuracy of the near real-time detection MLP-BP network is 96.6%, and the accuracies for the detailed MLP-BP neural network for Hong Kong and Taiwan is 74.8%. This newly automated multi-scale hybrid method can be used to give advance near real-time mapping of dust storms for environmental authorities and the public. It is also beneficial for identifying spatial locations of adverse air quality conditions, and estimates of low visibility associated with dust events for port and airport authorities.

  17. Multi-scale Model of Residual Strength of 2D Plain Weave C/SiC Composites in Oxidation Atmosphere

    NASA Astrophysics Data System (ADS)

    Chen, Xihui; Sun, Zhigang; Sun, Jianfen; Song, Yingdong

    2017-02-01

    Multi-scale models play an important role in capturing the nonlinear response of woven carbon fiber reinforced ceramic matrix composites. In plain weave carbon fiber/silicon carbon (C/SiC) composites, the carbon fibers and interphases will be oxidized at elevated temperature and the strength of the composite will be degraded when oxygen enters micro-cracks formed in the as-produced parts due to the mismatch in thermal properties between constituents. As a result of the oxidation on fiber surface, fiber shows a notch-like morphology. In this paper, the change rule of fiber notch depth is fitted by circular function. And a multi-scale model based upon the change rule of fiber notch depth is developed to simulate the residual strength and post-oxidation stress-strain curves of the composite. The multi-scale model is able to accurately predict the residual strength and post-oxidation stress-strain curves of the composite. Besides, the simulated residual strength and post-oxidation stress-strain curves of 2D plain weave C/SiC composites in oxidation atmosphere show good agreements with experimental results. Furthermore, the oxidation time and temperature of the composite are investigated to show their influences upon the residual strength and post-oxidation stress-strain curves of plain weave C/SiC composites.

  18. Multi-scale Model of Residual Strength of 2D Plain Weave C/SiC Composites in Oxidation Atmosphere

    NASA Astrophysics Data System (ADS)

    Chen, Xihui; Sun, Zhigang; Sun, Jianfen; Song, Yingdong

    2016-06-01

    Multi-scale models play an important role in capturing the nonlinear response of woven carbon fiber reinforced ceramic matrix composites. In plain weave carbon fiber/silicon carbon (C/SiC) composites, the carbon fibers and interphases will be oxidized at elevated temperature and the strength of the composite will be degraded when oxygen enters micro-cracks formed in the as-produced parts due to the mismatch in thermal properties between constituents. As a result of the oxidation on fiber surface, fiber shows a notch-like morphology. In this paper, the change rule of fiber notch depth is fitted by circular function. And a multi-scale model based upon the change rule of fiber notch depth is developed to simulate the residual strength and post-oxidation stress-strain curves of the composite. The multi-scale model is able to accurately predict the residual strength and post-oxidation stress-strain curves of the composite. Besides, the simulated residual strength and post-oxidation stress-strain curves of 2D plain weave C/SiC composites in oxidation atmosphere show good agreements with experimental results. Furthermore, the oxidation time and temperature of the composite are investigated to show their influences upon the residual strength and post-oxidation stress-strain curves of plain weave C/SiC composites.

  19. Multi-scale Modeling of Power Plant Plume Emissions and Comparisons with Observations

    NASA Astrophysics Data System (ADS)

    Costigan, K. R.; Lee, S.; Reisner, J.; Dubey, M. K.; Love, S. P.; Henderson, B. G.; Chylek, P.

    2011-12-01

    The Remote Sensing Verification Project (RSVP) test-bed located in the Four Corners region of Arizona, Utah, Colorado, and New Mexico offers a unique opportunity to develop new approaches for estimating emissions of CO2. Two major power plants located in this area produce very large signals of co-emitted CO2 and NO2 in this rural region. In addition to the Environmental Protection Agency (EPA) maintaining Continuous Emissions Monitoring Systems (CEMS) on each of the power plant stacks, the RSVP program has deployed an array of in-situ and remote sensing instruments, which provide both point and integrated measurements. To aid in the synthesis and interpretation of the measurements, a multi-scale atmospheric modeling approach is implemented, using two atmospheric numerical models: the Weather Research and Forecasting Model with chemistry (WRF-Chem; Grell et al., 2005) and the HIGRAD model (Reisner et al., 2003). The high fidelity HIGRAD model incorporates a multi-phase Lagrangian particle based approach to track individual chemical species of stack plumes at ultra-high resolution, using an adaptive mesh. It is particularly suited to model buoyancy effects and entrainment processes at the edges of the power plant plumes. WRF-Chem is a community model that has been applied to a number of air quality problems and offers several physical and chemical schemes that can be used to model the transport and chemical transformation of the anthropogenic plumes out of the local region. Multiple nested grids employed in this study allow the model to incorporate atmospheric variability ranging from synoptic scales to micro-scales (~200 m), while including locally developed flows influenced by the nearby complex terrain of the San Juan Mountains. The simulated local atmospheric dynamics are provided to force the HIGRAD model, which links mesoscale atmospheric variability to the small-scale simulation of the power plant plumes. We will discuss how these two models are applied and

  20. A Multi-Scale Modeling Framework for Shear Initiated Reactions in Energetic Materials

    DTIC Science & Technology

    2013-07-01

    sample problem is presented as a verification exercise. 15. SUBJECT TERMS Multi-scale, shear initiation, energetic materials, high explosives...systems. Requirements of energetic materials for future weapons have become increasingly stringent. It is desired to have high energy density output...towards self- sustaining reaction depends on the formation of local regions of elevated thermal energy; also referred to as hot spots. For high

  1. MEGAPOLI: concept and first results of multi-scale modelling of megacity impacts

    NASA Astrophysics Data System (ADS)

    Baklanov, A. A.; Lawrence, M.; Pandis, S.

    2009-09-01

    major city, Paris, performing detailed analysis for 12 megacities with existing air quality datasets and investigate the effects of all megacities on climate and global atmospheric chemistry. The project focuses on the multi-scale modelling of interacting meteorology and air quality, spanning the range from emissions to air quality, effects on climate, and feedbacks and mitigation potentials. Our hypothesis is that megacities around the world have an impact on air quality not only locally, but also regionally and globally and therefore can also influence the climate of our planet. Some of the links between megacities, air quality and climate are reasonably well-understood. However, a complete quantitative picture of these interactions is clearly missing. Understanding and quantifying these missing links is the focus of MEGAPOLI. The current status and modeling results after the first project year on examples of Paris and other European megacities are discussed.

  2. Numerical Modeling of Multi-scale Organized Convection and an Inertia-gravity Wave Observed during YOTC

    NASA Astrophysics Data System (ADS)

    Liu, Changhai; Moncrieff, Mitchell

    2015-04-01

    A multi-scale organized convection event was observed in the eastern Indian Ocean during 9-11 April, 2009. This system initiated near the western coast of Sumatra, was embedded in an active MJO, traveled westward at roughly 10 m/s, and lasted for about 2 days. To investigate the thermodynamic and kinematic structure of this multi-scale system, cloud-system resolving simulations were conducted using the Weather Research and Forecasting (WRF) model forced by ERA-Interim reanalysis. Results indicated that the WRF model accurately reproduced many features documented by TRMM observations, such as the timing and location, the propagation behavior, the life cycle, and in particular, the multi-scale structure consisting of a westward-propagating synoptic-scale organization (envelope) and a series of oppositely propagating mesoscale convective systems as well as the embedded small-scale convective elements. Preliminary analysis suggests that the organized convection is coupled to a lower-tropospheric equatorial inertia-gravity wave of approximately 12-degree zonal wavelength. Moreover, the associated perturbations evince rearward (eastward) tilting with respect to the propagation direction. More detailed analysis, including the energetics, presently under way will be presented in the meeting.

  3. Use of ARM Data to address the Climate Change Further Development and Applications of A Multi-scale Modeling Framework

    SciTech Connect

    David A. Randall; Marat Khairoutdinov

    2007-12-14

    The Colorado State University (CSU) Multi-scale Modeling Framework (MMF) is a new type of general circulation model (GCM) that replaces the conventional parameterizations of convection, clouds and boundary layer with a cloud-resolving model (CRM) embedded into each grid column. The MMF that we have been working with is a “super-parameterized” version of the Community Atmosphere Model (CAM). As reported in the publications listed below, we have done extensive work with the model. We have explored the MMF’s performance in several studies, including an AMIP run and a CAPT test, and we have applied the MMF to an analysis of climate sensitivity.

  4. Overview of Computer-Aided Engineering of Batteries and Introduction to Multi-Scale, Multi-Dimensional Modeling of Li-Ion Batteries (Presentation)

    SciTech Connect

    Pesaran, A.; Kim, G. H.; Smith, K.; Santhanagopalan, S.; Lee, K. J.

    2012-05-01

    This 2012 Annual Merit Review presentation gives an overview of the Computer-Aided Engineering of Batteries (CAEBAT) project and introduces the Multi-Scale, Multi-Dimensional model for modeling lithium-ion batteries for electric vehicles.

  5. Development of a multi-scale data assimilation system for model-observation integration and climate model evaluation (Invited)

    NASA Astrophysics Data System (ADS)

    Li, Z.; Liu, Y.; Lin, W.; Vogelmann, A. M.; Feng, S.; Fridlind, A. M.

    2013-12-01

    To improve our understanding and the representation of subgrid processes in climate models, an increasing number of ground-based long-term observing systems have been established. These systems focus on detailed measurements over a domain of a typical climate model grid size. An example is the US DOE Atmospheric Radiation Measurement (ARM) program, which has been collecting data related to radiation, clouds and precipitation at three primary sites, the Southern Great Plains (SGP) of the USA, the North Slope of Alaska, and the Tropical West Pacific, for approximately 20 years. A well-established approach to use ARM-like measurements in climate model evaluation is jointly using the Single Column Model (SCM), Cloud Resolving Models (CRMs), and/or large eddy simulations (LESs). To enhance the effectiveness of this approach, we have developed multi-scale data assimilation (MS-DA) system on top of the NCEP Gridpoint Statistical Interpolation (GSI) System and implemented in the Weather Research and Forecasting (WRF) model at the cloud resolving resolution (WRF-CRM) over the ARM Climate Research Facility's Southern Great Plains (SGP) site. It is demonstrated that the MS-DA effectively assimilate the dense ARM in-situ observations and high-resolution satellite data, thus significantly reducing uncertainties in the WRF CRM simulation. We have used the WRF CRM simulation constrained by the MS-DA to derive multi-scale forcing that is used to drive SCMs, CRMs, and LESs, expand the large scale forcing parameters to hydrometeors that are not provided in the existing continuous forcing product, and characterize dependency of large-scale forcing on domain-size that represents SCM grid-sizes, sub-grid processes, and cloud-regimes.

  6. Storm surge simulation along the U.S. East and Gulf Coasts using a multi-scale numerical model approach

    NASA Astrophysics Data System (ADS)

    Xu, Hongzhou; Zhang, Keqi; Shen, Jian; Li, Yuepeng

    2010-12-01

    The effectiveness of simulating surge inundation using the Eulerian-Lagrangian circulation (ELCIRC) model over multi-scale unstructured grids was examined in this study. The large domain model grid encompasses the western North Atlantic Ocean, the Gulf of Mexico, and the Caribbean Sea to appropriately account for remote and resonance effects during hurricane events and simplify the specification of the open boundary condition. The U.S. East and Gulf Coasts were divided into 12 overlapping basins with fine-resolution (up to 30 × 30 m) grids to model overland surge flooding. These overlapping basins have different fine-resolution grids near the coastal region, but have an identical coarse-resolution grid in the offshore region within the large model domain. Thus, the storm surge prediction can be conducted without reducing computation efficiency by executing multiple model runs with local fine-resolution grids where potential hurricane landfalls may occur. The capability of the multi-scale approach was examined by simulating storm surge caused by Hurricanes Andrew (1992) and Isabel (2003) along the South Florida coast and in the Chesapeake Bay. Comparisons between simulated and observed results suggest that multi-scale models proficiently simulated storm surges in the Biscayne Bay and the Chesapeake Bay during two hurricanes. A series of sensitivity tests demonstrated that the simulation of surge flooding was improved when LiDAR topographic data and special bottom drag coefficient values for mangrove forests were employed. The tests also showed that appropriate representation of linear hydrologic features is important for computing surge inundation in an urban area.

  7. Multi-scale modeling of microstructure dependent intergranular brittle fracture using a quantitative phase-field based method

    SciTech Connect

    Chakraborty, Pritam; Zhang, Yongfeng; Tonks, Michael R.

    2015-12-07

    In this study, the fracture behavior of brittle materials is strongly influenced by their underlying microstructure that needs explicit consideration for accurate prediction of fracture properties and the associated scatter. In this work, a hierarchical multi-scale approach is pursued to model microstructure sensitive brittle fracture. A quantitative phase-field based fracture model is utilized to capture the complex crack growth behavior in the microstructure and the related parameters are calibrated from lower length scale atomistic simulations instead of engineering scale experimental data. The workability of this approach is demonstrated by performing porosity dependent intergranular fracture simulations in UO2 and comparing the predictions with experiments.

  8. Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite

    SciTech Connect

    Pogorelov, N.V.; Borovikov, S. N.; Bedford, M. C.; Heerikhuisen, J.; Kim, T. K.; Kryukov, I. A.; Zank, G. P.

    2013-04-01

    Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS) is a package of numerical codes capable of performing adaptive mesh refinement simulations of complex plasma flows in the presence of discontinuities and charge exchange between ions and neutral atoms. The flow of the ionized component is described with the ideal MHD equations, while the transport of atoms is governed either by the Boltzmann equation or multiple Euler gas dynamics equations. We have enhanced the code with additional physical treatments for the transport of turbulence and acceleration of pickup ions in the interplanetary space and at the termination shock. In this article, we present the results of our numerical simulation of the solar wind (SW) interaction with the local interstellar medium (LISM) in different time-dependent and stationary formulations. Numerical results are compared with the Ulysses, Voyager, and OMNI observations. Finally, the SW boundary conditions are derived from in-situ spacecraft measurements and remote observations.

  9. Pricing credit default swaps under a multi-scale stochastic volatility model

    NASA Astrophysics Data System (ADS)

    Chen, Wenting; He, Xinjiang

    2017-02-01

    In this paper, we consider the pricing of credit default swaps (CDSs) with the reference asset driven by a geometric Brownian motion with a multi-scale stochastic volatility (SV), which is a two-factor volatility process with one factor controlling the fast time scale and the other representing the slow time scale. A key feature of the current methodology is to establish an equivalence relationship between the CDS and the down-and-out binary option through the discussion of "no default" probability, while balancing the two SV processes with the perturbation method. An approximate but closed-form pricing formula for the CDS contract is finally obtained, whose accuracy is in the order of O(ɛ + δ +√{ ɛδ }) .

  10. Multi-scale modeling of the phase diagram of Human Immunoglobulin

    NASA Astrophysics Data System (ADS)

    Tuchman, Mark; Buldyrev, Sergey; Wang, Ying; Lomakin, Aleksey; Benedek, George B.

    2014-03-01

    Human Immunoglobulin antibodies IGg is a Y-shape trimer consisting of three folded protein globules, connected by two polypeptide hinges in random conformations linked by disulfide bonds. The solubility and crystallization phase diagrams of immunoglobulin are crucial in understanding various pathological conditions. It is experimentally known that the critical volume fraction of immunoglobulin is three times smaller than for typical globular proteins. In order to explain this phenomenon, we perform a multi-scale molecular dynamic (MD) simulations. First we produce all atom simulations of the hinges and compute the distribution of their end-to-end distances. Using these results we construct a simple effective bond potential and study a phase diagram of a system of three sticky hard-spheres linked by these bonds by discrete MD simulations. The results are in good agreement with the experiment.

  11. Toward Multi-scale Modeling and simulation of conduction in heterogeneous materials

    SciTech Connect

    Lechman, Jeremy B.; Battaile, Corbett Chandler.; Bolintineanu, Dan; Cooper, Marcia A.; Erikson, William W.; Foiles, Stephen M.; Kay, Jeffrey J; Phinney, Leslie M.; Piekos, Edward S.; Specht, Paul Elliott; Wixom, Ryan R.; Yarrington, Cole

    2015-01-01

    This report summarizes a project in which the authors sought to develop and deploy: (i) experimental techniques to elucidate the complex, multiscale nature of thermal transport in particle-based materials; and (ii) modeling approaches to address current challenges in predicting performance variability of materials (e.g., identifying and characterizing physical- chemical processes and their couplings across multiple length and time scales, modeling information transfer between scales, and statically and dynamically resolving material structure and its evolution during manufacturing and device performance). Experimentally, several capabilities were successfully advanced. As discussed in Chapter 2 a flash diffusivity capability for measuring homogeneous thermal conductivity of pyrotechnic powders (and beyond) was advanced; leading to enhanced characterization of pyrotechnic materials and properties impacting component development. Chapter 4 describes success for the first time, although preliminary, in resolving thermal fields at speeds and spatial scales relevant to energetic components. Chapter 7 summarizes the first ever (as far as the authors know) application of TDTR to actual pyrotechnic materials. This is the first attempt to actually characterize these materials at the interfacial scale. On the modeling side, new capabilities in image processing of experimental microstructures and direct numerical simulation on complicated structures were advanced (see Chapters 3 and 5). In addition, modeling work described in Chapter 8 led to improved prediction of interface thermal conductance from first principles calculations. Toward the second point, for a model system of packed particles, significant headway was made in implementing numerical algorithms and collecting data to justify the approach in terms of highlighting the phenomena at play and pointing the way forward in developing and informing the kind of modeling approach originally envisioned (see Chapter 6). In

  12. Multi-scale Predictability with a New Coupled Non-hydrostatic Global Model over the Arctic Annual Report

    DTIC Science & Technology

    2013-09-30

    DATES COVERED 00-00-2013 to 00-00-2013 4 . TITLE AND SUBTITLE Multi-scale Predictability with a New Coupled Non-hydrostatic Global Model over...is approximately 4 in (a) and 7 in (b), these meshes are subsequently referred to as ‘x4’ and ‘x7’ for brevity. Table 2: Summary of select...shows that during this stage of cyclone development, it is located over the coastline of Siberia and an unfrozen section of the Arctic Ocean (Fig. 4

  13. Final Progress Report: FRACTURE AND SUBCRITICAL DEBONDING IN THIN LAYERED STRUCTURES: EXPERIMENTS AND MULTI-SCALE MODELING

    SciTech Connect

    Reinhold H. Dauskardt

    2005-08-30

    Final technical report detailing unique experimental and multi-scale computational modeling capabilities developed to study fracture and subcritical cracking in thin-film structures. Our program to date at Stanford has studied the mechanisms of fracture and fatigue crack-growth in structural ceramics at high temperature, bulk and thin-film glasses in selected moist environments where we demonstrated the presence of a true mechanical fatigue effect in some glass compositions. We also reported on the effects of complex environments and fatigue loading on subcritical cracking that effects the reliability of MEMS and other micro-devices using novel micro-machined silicon specimens and nanomaterial layers.

  14. Magnetic hysteresis at the domain scale of a multi-scale material model for magneto-elastic behaviour

    NASA Astrophysics Data System (ADS)

    Vanoost, D.; Steentjes, S.; Peuteman, J.; Gielen, G.; De Gersem, H.; Pissoort, D.; Hameyer, K.

    2016-09-01

    This paper proposes a multi-scale energy-based material model for poly-crystalline materials. Describing the behaviour of poly-crystalline materials at three spatial scales of dominating physical mechanisms allows accounting for the heterogeneity and multi-axiality of the material behaviour. The three spatial scales are the poly-crystalline, grain and domain scale. Together with appropriate scale transitions rules and models for local magnetic behaviour at each scale, the model is able to describe the magneto-elastic behaviour (magnetostriction and hysteresis) at the macroscale, although the data input is merely based on a set of physical constants. Introducing a new energy density function that describes the demagnetisation field, the anhysteretic multi-scale energy-based material model is extended to the hysteretic case. The hysteresis behaviour is included at the domain scale according to the micro-magnetic domain theory while preserving a valid description for the magneto-elastic coupling. The model is verified using existing measurement data for different mechanical stress levels.

  15. A multi-scale model of the oxygen reduction reaction on highly active graphene nanosheets in alkaline conditions

    NASA Astrophysics Data System (ADS)

    Vazquez-Arenas, Jorge; Ramos-Sanchez, Guadalupe; Franco, Alejandro A.

    2016-10-01

    A multi-scale model based on a mean field approach, is proposed to describe the ORR mechanism on N-GN catalysts in alkaline media. The model implements activation energies calculated with Density Functional Theory (DFT) at the atomistic level, and scales up them into a continuum framework describing the cathode/electrolyte interface at the mesoscale level. The model also considers mass and momentum transports arising in the region next to the rotating electrode for all ionic species and O2; correction of potential drop and electrochemical double-layer capacitance. Most fitted parameters describing the kinetics of ORR elementary reactions are sensitive in the multi-scale model, which results from the incorporation of activation energies using the mean field method, unlike single-scale modelling Errors in the deviations from activation energies are found to be moderate, except for the elementary step (2) related to the formation of O2ads, which can be assigned to the inherent DFT limitations. The consumption of O2ads to form OOHads is determined as the rate-determining step as a result of its highest energy barrier (163.10 kJ mol-1) in the system, the largest error obtained for the deviation from activation energy (28.15%), and high sensitivity. This finding is confirmed with the calculated surface concentration and coverage of electroactive species.

  16. Multi-scale modeling of Arabidopsis thaliana response to different CO2 conditions: From gene expression to metabolic flux.

    PubMed

    Liu, Lin; Shen, Fangzhou; Xin, Changpeng; Wang, Zhuo

    2016-01-01

    Multi-scale investigation from gene transcript level to metabolic activity is important to uncover plant response to environment perturbation. Here we integrated a genome-scale constraint-based metabolic model with transcriptome data to explore Arabidopsis thaliana response to both elevated and low CO2 conditions. The four condition-specific models from low to high CO2 concentrations show differences in active reaction sets, enriched pathways for increased/decreased fluxes, and putative post-transcriptional regulation, which indicates that condition-specific models are necessary to reflect physiological metabolic states. The simulated CO2 fixation flux at different CO2 concentrations is consistent with the measured Assimilation-CO2intercellular curve. Interestingly, we found that reactions in primary metabolism are affected most significantly by CO2 perturbation, whereas secondary metabolic reactions are not influenced a lot. The changes predicted in key pathways are consistent with existing knowledge. Another interesting point is that Arabidopsis is required to make stronger adjustment on metabolism to adapt to the more severe low CO2 stress than elevated CO2 . The challenges of identifying post-transcriptional regulation could also be addressed by the integrative model. In conclusion, this innovative application of multi-scale modeling in plants demonstrates potential to uncover the mechanisms of metabolic response to different conditions.

  17. Two-Phase Fluid Leakage through Faults Using a Multi-Scale Analytical-Numerical Modeling Approach

    NASA Astrophysics Data System (ADS)

    Kang, M.; Nordbotten, J. M.; Doster, F.; Celia, M. A.

    2014-12-01

    Fluid flow through faults must be considered in many applications including geologic storage of carbon dioxide (CO2), deep storage of hazardous waste, groundwater contamination, and petroleum engineering. In the case of CO2 storage, the presence of faults is of concern, because they can act as leakage pathways. Therefore, modeling tools that can accurately and efficiently quantify fluid leakage through faults in basin-scale models are necessary. In basin-scale models, the flow around and through faults is a local-scale process and this local-scale variation is important when determining leakage rates. We present a multi-scale modeling approach based on embedding local-scale analytical solutions within basin-scale numerical models. At the local scale, steady-state analytical solutions that represent fluid flow in the vicinity of leaky faults, including any vertical flow effects, are derived. Using both numerical simulations and analytical solutions, an empirical model representing fault properties, permeabilities and widths, is also developed. The combination of this empirical fault model and the analytical solutions captures the local-scale effects of leakage through faults. The local-scale model is used within a multi-scale modeling framework to determine the flow in and around faults and the associated local-scale pressure and saturation corrections that are applied to the coarse model. Here, a fault is viewed as a 2-D surface on one side of a coarse-scale grid block. The corrections relate local-scale pressure and saturation at the fault to coarse-scale pressures and saturations in numerical grid blocks. The corrections are used to determine the vertical and lateral flow in the fault and horizontal flows perpendicular and parallel to the fault in the grid block. At every coarse-scale time step, the local-scale fault model is implemented using the coarse-scale information from the previous time step. The resulting leakage rates and pressure and saturation

  18. Modeling Complex Biological Flows in Multi-Scale Systems using the APDEC Framework

    SciTech Connect

    Trebotich, D

    2006-06-24

    We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA-laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.

  19. Simulated village locations in Thailand: A multi-scale model including a neural network approach.

    PubMed

    Tang, Wenwu; Malanson, George P; Entwisle, Barbara

    2009-04-01

    The simulation of rural land use systems, in general, and rural settlement dynamics in particular has developed with synergies of theory and methods for decades. Three current issues are: linking spatial patterns and processes, representing hierarchical relations across scales, and considering nonlinearity to address complex non-stationary settlement dynamics. We present a hierarchical simulation model to investigate complex rural settlement dynamics in Nang Rong, Thailand. This simulation uses sub-models to allocate new villages at three spatial scales. Regional and sub-regional models, which involve a nonlinear space-time autoregressive model implemented in a neural network approach, determine the number of new villages to be established. A dynamic village niche model, establishing pattern-process link, was designed to enable the allocation of villages into specific locations. Spatiotemporal variability in model performance indicates the pattern of village location changes as a settlement frontier advances from rice-growing lowlands to higher elevations. Experiments results demonstrate this simulation model can enhance our understanding of settlement development in Nang Rong and thus gain insight into complex land use systems in this area.

  20. Simulated village locations in Thailand: A multi-scale model including a neural network approach

    PubMed Central

    Malanson, George P.; Entwisle, Barbara

    2010-01-01

    The simulation of rural land use systems, in general, and rural settlement dynamics in particular has developed with synergies of theory and methods for decades. Three current issues are: linking spatial patterns and processes, representing hierarchical relations across scales, and considering nonlinearity to address complex non-stationary settlement dynamics. We present a hierarchical simulation model to investigate complex rural settlement dynamics in Nang Rong, Thailand. This simulation uses sub-models to allocate new villages at three spatial scales. Regional and sub-regional models, which involve a nonlinear space-time autoregressive model implemented in a neural network approach, determine the number of new villages to be established. A dynamic village niche model, establishing pattern-process link, was designed to enable the allocation of villages into specific locations. Spatiotemporal variability in model performance indicates the pattern of village location changes as a settlement frontier advances from rice-growing lowlands to higher elevations. Experiments results demonstrate this simulation model can enhance our understanding of settlement development in Nang Rong and thus gain insight into complex land use systems in this area. PMID:21399748

  1. Nano finite element modeling of the mechanical behavior of biocomposites using multi-scale (virtual internal bond) material models

    PubMed Central

    Thiagarajan, Ganesh; Deshmukh, Kavita; Wang, Yong; Misra, A.; Katz, J. Lawrence; Spencer, Paulette

    2007-01-01

    It is evident that biocomposites, specifically mineralized Type-I collagen fibrils, have strong mechanical properties, such as a desirable combination of elastic modulus, fracture toughness, and fracture strength. The mineral Hydroxyapatite [Hap] by itself is stiffer, and it is not clear whether a collagen fiber by itself has a lower breaking strength than the mineralized fiber. Hence, the objective of this paper is to develop, outline, apply, and demonstrate issues involving a new nano explicit finite element based framework, by which the mechanical behavior of mineralized collagen fibrils and their constituents can be studied. A multi-scale virtual internal bond model is used to model the material behavior and failure of such biocomposites. In this research two models have been studied. The first model attempts to illustrate the hypothesis that materials are less sensitive to flaws at nanoscale and the second model studies the mechanical behavior of a nano sized dahlite mineral crystal commonly found in collagen fibril. Two important implementation characteristics have been introduced and illustrated, namely that scaled properties can be used at the micro and nano length scales along with scaled dimensions and secondly the loading time can be appropriately scaled without the loading becoming a dynamic loading. PMID:17450580

  2. Concurrent multi-scale design optimization of composite frame structures using the Heaviside penalization of discrete material model

    NASA Astrophysics Data System (ADS)

    Yan, Jun; Duan, Zunyi; Lund, Erik; Zhao, Guozhong

    2016-06-01

    This paper deals with the concurrent multi-scale optimization design of frame structure composed of glass or carbon fiber reinforced polymer laminates. In the composite frame structure, the fiber winding angle at the micro-material scale and the geometrical parameter of components of the frame in the macro-structural scale are introduced as the independent variables on the two geometrical scales. Considering manufacturing requirements, discrete fiber winding angles are specified for the micro design variable. The improved Heaviside penalization discrete material optimization interpolation scheme has been applied to achieve the discrete optimization design of the fiber winding angle. An optimization model based on the minimum structural compliance and the specified fiber material volume constraint has been established. The sensitivity information about the two geometrical scales design variables are also deduced considering the characteristics of discrete fiber winding angles. The optimization results of the fiber winding angle or the macro structural topology on the two single geometrical scales, together with the concurrent two-scale optimization, is separately studied and compared in the paper. Numerical examples in the paper show that the concurrent multi-scale optimization can further explore the coupling effect between the macro-structure and micro-material of the composite to achieve an ultra-light design of the composite frame structure. The novel two geometrical scales optimization model provides a new opportunity for the design of composite structure in aerospace and other industries.

  3. Uncertainty Quantification and Management for Multi-scale Nuclear Materials Modeling

    SciTech Connect

    McDowell, David; Deo, Chaitanya; Zhu, Ting; Wang, Yan

    2015-10-21

    Understanding and improving microstructural mechanical stability in metals and alloys is central to the development of high strength and high ductility materials for cladding and cores structures in advanced fast reactors. Design and enhancement of radiation-induced damage tolerant alloys are facilitated by better understanding the connection of various unit processes to collective responses in a multiscale model chain, including: dislocation nucleation, absorption and desorption at interfaces; vacancy production, radiation-induced segregation of Cr and Ni at defect clusters (point defect sinks) in BCC Fe-Cr ferritic/martensitic steels; investigation of interaction of interstitials and vacancies with impurities (V, Nb, Ta, Mo, W, Al, Si, P, S); time evolution of swelling (cluster growth) phenomena of irradiated materials; and energetics and kinetics of dislocation bypass of defects formed by interstitial clustering and formation of prismatic loops, informing statistical models of continuum character with regard to processes of dislocation glide, vacancy agglomeration and swelling, climb and cross slip.

  4. Multi-scale modelling of supercapacitors: From molecular simulations to a transmission line model

    NASA Astrophysics Data System (ADS)

    Pean, C.; Rotenberg, B.; Simon, P.; Salanne, M.

    2016-09-01

    We perform molecular dynamics simulations of a typical nanoporous-carbon based supercapacitor. The organic electrolyte consists in 1-ethyl-3-methylimidazolium and hexafluorophosphate ions dissolved in acetonitrile. We simulate systems at equilibrium, for various applied voltages. This allows us to determine the relevant thermodynamic (capacitance) and transport (in-pore resistivities) properties. These quantities are then injected in a transmission line model for testing its ability to predict the charging properties of the device. The results from this macroscopic model are in good agreement with non-equilibrium molecular dynamics simulations, which validates its use for interpreting electrochemical impedance experiments.

  5. Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite

    DOE PAGES

    Pogorelov, N.V.; Borovikov, S. N.; Bedford, M. C.; ...

    2013-04-01

    Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS) is a package of numerical codes capable of performing adaptive mesh refinement simulations of complex plasma flows in the presence of discontinuities and charge exchange between ions and neutral atoms. The flow of the ionized component is described with the ideal MHD equations, while the transport of atoms is governed either by the Boltzmann equation or multiple Euler gas dynamics equations. We have enhanced the code with additional physical treatments for the transport of turbulence and acceleration of pickup ions in the interplanetary space and at the termination shock. In this article, we present themore » results of our numerical simulation of the solar wind (SW) interaction with the local interstellar medium (LISM) in different time-dependent and stationary formulations. Numerical results are compared with the Ulysses, Voyager, and OMNI observations. Finally, the SW boundary conditions are derived from in-situ spacecraft measurements and remote observations.« less

  6. Multi-Scale Modeling, Surrogate-Based Analysis, and Optimization of Lithium-Ion Batteries for Vehicle Applications

    NASA Astrophysics Data System (ADS)

    Du, Wenbo

    A common attribute of electric-powered aerospace vehicles and systems such as unmanned aerial vehicles, hybrid- and fully-electric aircraft, and satellites is that their performance is usually limited by the energy density of their batteries. Although lithium-ion batteries offer distinct advantages such as high voltage and low weight over other battery technologies, they are a relatively new development, and thus significant gaps in the understanding of the physical phenomena that govern battery performance remain. As a result of this limited understanding, batteries must often undergo a cumbersome design process involving many manual iterations based on rules of thumb and ad-hoc design principles. A systematic study of the relationship between operational, geometric, morphological, and material-dependent properties and performance metrics such as energy and power density is non-trivial due to the multiphysics, multiphase, and multiscale nature of the battery system. To address these challenges, two numerical frameworks are established in this dissertation: a process for analyzing and optimizing several key design variables using surrogate modeling tools and gradient-based optimizers, and a multi-scale model that incorporates more detailed microstructural information into the computationally efficient but limited macro-homogeneous model. In the surrogate modeling process, multi-dimensional maps for the cell energy density with respect to design variables such as the particle size, ion diffusivity, and electron conductivity of the porous cathode material are created. A combined surrogate- and gradient-based approach is employed to identify optimal values for cathode thickness and porosity under various operating conditions, and quantify the uncertainty in the surrogate model. The performance of multiple cathode materials is also compared by defining dimensionless transport parameters. The multi-scale model makes use of detailed 3-D FEM simulations conducted at the

  7. The North American Carbon Program Multi-scale Synthesis and Terrestrial Model Intercomparison Project – Part 2: Environmental driver data

    SciTech Connect

    Wei, Yaxing; Liu, Shishi; Huntzinger, Deborah N.; Michalak, Anna M.; Viovy, Nicolas; Post, Wilfred M.; Schwalm, Christopher R.; Schaeffer, Kevin; Jacobson, Andrew R.; Lu, Chaoqun; Tian, Hanqin; Ricciuto, Daniel M.; Cook, Robert B.; Mao, Jiafu; Shi, Xiaoying

    2014-12-05

    Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model model and model observation comparisons. In this article, we describe the global and North American environmental driver data sets prepared for the MsTMIP activity to both support their use in MsTMIP and make these data, along with the processes used in selecting/processing these data, accessible to a broader audience. Based on project needs and lessons learned from past model intercomparison activities, we compiled climate, atmospheric CO2 concentrations, nitrogen deposition, land use and land cover change (LULCC), C3 / C4 grasses fractions, major crops, phenology and soil data into a standard format for global (0.5⁰ x 0.5⁰ resolution) and regional (North American: 0.25⁰ x 0.25⁰ resolution) simulations. In order to meet the needs of MsTMIP, improvements were made to several of the original environmental data sets, by improving the quality, and/or changing their spatial and temporal coverage, and resolution. The resulting standardized model driver data sets are being used by over 20 different models participating in MsTMIP. Lastly, the data are archived at the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, http://daac.ornl.gov) to provide long-term data management and distribution.

  8. The North American Carbon Program Multi-scale Synthesis and Terrestrial Model Intercomparison Project - Part 2: Environmental driver data

    NASA Astrophysics Data System (ADS)

    Wei, Y.; Liu, S.; Huntzinger, D. N.; Michalak, A. M.; Viovy, N.; Post, W. M.; Schwalm, C. R.; Schaefer, K.; Jacobson, A. R.; Lu, C.; Tian, H.; Ricciuto, D. M.; Cook, R. B.; Mao, J.; Shi, X.

    2013-11-01

    Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM model skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model-model and model-observation comparisons. This paper describes the global and North American environmental driver data sets prepared for the MsTMIP activity to both support their use in MsTMIP and make these data, along with the processes used in selecting/processing these data, accessible to a broader audience. Based on project needs, we compiled climate, atmospheric CO2 concentrations, nitrogen deposition, land-use and land-cover change (LULCC), C3/C4 grasses fractions, major crops, phenology, and soil data into a standard format for global (0.5° x 0.5° resolution) and regional (North American, 0.25° x 0.25° resolution) simulations. In order to meet the needs of MsTMIP, improvements were made to several of the original environmental data sets, by changing the quality, the spatial and temporal coverage, resolution, or a combination of these. The resulting standardized model driver data sets are being used by over 20 different models participating MsTMIP. The data are archived at the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, http://daac.ornl.gov) to provide long-term data management and distribution.

  9. The North American Carbon Program Multi-scale Synthesis and Terrestrial Model Intercomparison Project - Part 2: Environmental driver data

    NASA Astrophysics Data System (ADS)

    Wei, Y.; Liu, S.; Huntzinger, D. N.; Michalak, A. M.; Viovy, N.; Post, W. M.; Schwalm, C. R.; Schaefer, K.; Jacobson, A. R.; Lu, C.; Tian, H.; Ricciuto, D. M.; Cook, R. B.; Mao, J.; Shi, X.

    2014-12-01

    Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model-model and model-observation comparisons. This paper describes the global and North American environmental driver data sets prepared for the MsTMIP activity to both support their use in MsTMIP and make these data, along with the processes used in selecting/processing these data, accessible to a broader audience. Based on project needs and lessons learned from past model intercomparison activities, we compiled climate, atmospheric CO2 concentrations, nitrogen deposition, land use and land cover change (LULCC), C3 / C4 grasses fractions, major crops, phenology and soil data into a standard format for global (0.5° × 0.5° resolution) and regional (North American: 0.25° × 0.25° resolution) simulations. In order to meet the needs of MsTMIP, improvements were made to several of the original environmental data sets, by improving the quality, and/or changing their spatial and temporal coverage, and resolution. The resulting standardized model driver data sets are being used by over 20 different models participating in MsTMIP. The data are archived at the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, http://daac.ornl.gov) to provide long-term data management and distribution.

  10. The North American Carbon Program Multi-scale Synthesis and Terrestrial Model Intercomparison Project – Part 2: Environmental driver data

    DOE PAGES

    Wei, Yaxing; Liu, Shishi; Huntzinger, Deborah N.; ...

    2014-12-05

    Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model model and model observation comparisons. Inmore » this article, we describe the global and North American environmental driver data sets prepared for the MsTMIP activity to both support their use in MsTMIP and make these data, along with the processes used in selecting/processing these data, accessible to a broader audience. Based on project needs and lessons learned from past model intercomparison activities, we compiled climate, atmospheric CO2 concentrations, nitrogen deposition, land use and land cover change (LULCC), C3 / C4 grasses fractions, major crops, phenology and soil data into a standard format for global (0.5⁰ x 0.5⁰ resolution) and regional (North American: 0.25⁰ x 0.25⁰ resolution) simulations. In order to meet the needs of MsTMIP, improvements were made to several of the original environmental data sets, by improving the quality, and/or changing their spatial and temporal coverage, and resolution. The resulting standardized model driver data sets are being used by over 20 different models participating in MsTMIP. Lastly, the data are archived at the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, http://daac.ornl.gov) to provide long-term data management and distribution.« less

  11. Multi-Scale Impact and Compression-After-Impact Modeling of Reinforced Benzoxazine/Epoxy Composites using Micromechanics Approach

    NASA Astrophysics Data System (ADS)

    Montero, Marc Villa; Barjasteh, Ehsan; Baid, Harsh K.; Godines, Cody; Abdi, Frank; Nikbin, Kamran

    A multi-scale micromechanics approach along with finite element (FE) model predictive tool is developed to analyze low-energy-impact damage footprint and compression-after-impact (CAI) of composite laminates which is also tested and verified with experimental data. Effective fiber and matrix properties were reverse-engineered from lamina properties using an optimization algorithm and used to assess damage at the micro-level during impact and post-impact FE simulations. Progressive failure dynamic analysis (PFDA) was performed for a two step-process simulation. Damage mechanisms at the micro-level were continuously evaluated during the analyses. Contribution of each failure mode was tracked during the simulations and damage and delamination footprint size and shape were predicted to understand when, where and why failure occurred during both impact and CAI events. The composite laminate was manufactured by the vacuum infusion of the aero-grade toughened Benzoxazine system into the fabric preform. Delamination footprint was measured using C-scan data from the impacted panels and compared with the predicated values obtained from proposed multi-scale micromechanics coupled with FE analysis. Furthermore, the residual strength was predicted from the load-displacement curve and compared with the experimental values as well.

  12. Multi-scale model of resistive-type superconducting fault current limiters based on 2G HTS coated conductors

    NASA Astrophysics Data System (ADS)

    Bonnard, Charles-Henri; Sirois, Frédéric; Lacroix, Christian; Didier, Gaëtan

    2017-01-01

    In order to plan the integration of superconducting fault current limiters (SFCLs) in power systems, accurate models of SFCLs must be made available in commercial power system transient simulators. In this context, we developed such a model for the EMTP-RV software package, a power system transient simulator widely used by power utilities. The model can be used with any resistive-type SFCL (rSFCL) made of high temperature superconductor (HTS) tapes, which are discretized in ‘electro-thermal elements’. Those elements consist solely of electric circuit components, and are used to represent portions of tape of various sizes and dimensions (a ‘multi-scale’ approach). Both the electrical and thermal behaviors of the tape are modeled, including interfacial effects, nonlinear properties of materials and heat transfer to the surrounding environment. Such a multi-scale model can simulate accurately both the local quench dynamics of HTS tapes (microscopic scale) and the global impact of the rSFCL on the power system (macroscopic/system scale). In this paper, the model is used to compute phenomena such as propagation velocity of a hot spot and heat diffusion through the thickness of the tape. Results were verified by comparing EMTP-RV results with finite element simulations. In addition to the development of the multi-scale model itself, which is the major contribution of this paper, the use of the model allowed us to determine the conditions of validity of the commonly used ‘homogenization’ of the thermal properties across the tape thickness. Indeed, when the current flowing into the rSFCL is slightly above its critical current I c (and up to 2{I}{{c}}), very important errors in the power waveforms arise, leading to potentially wrong decisions of protection systems. Homogenized thermal models should thus be used with great care in practice.

  13. Multi-scale hydrometeorological observation and modelling for flash-flood understanding

    NASA Astrophysics Data System (ADS)

    Braud, I.; Ayral, P.-A.; Bouvier, C.; Branger, F.; Delrieu, G.; Le Coz, J.; Nord, G.; Vandervaere, J.-P.; Anquetin, S.; Adamovic, M.; Andrieu, J.; Batiot, C.; Boudevillain, B.; Brunet, P.; Carreau, J.; Confoland, A.; Didon-Lescot, J.-F.; Domergue, J.-M.; Douvinet, J.; Dramais, G.; Freydier, R.; Gérard, S.; Huza, J.; Leblois, E.; Le Bourgeois, O.; Le Boursicaud, R.; Marchand, P.; Martin, P.; Nottale, L.; Patris, N.; Renard, B.; Seidel, J.-L.; Taupin, J.-D.; Vannier, O.; Vincendon, B.; Wijbrans, A.

    2014-02-01

    This paper presents a coupled observation and modelling strategy aiming at improving the understanding of processes triggering flash floods. This strategy is illustrated for the Mediterranean area using two French catchments (Gard and Ardèche) larger than 2000 km2. The approach is based on the monitoring of nested spatial scales: (1) the hillslope scale, where processes influencing the runoff generation and its concentration can be tackled; (2) the small to medium catchment scale (1-100 km2) where the impact of the network structure and of the spatial variability of rainfall, landscape and initial soil moisture can be quantified; (3) the larger scale (100-1000 km2) where the river routing and flooding processes become important. These observations are part of the HyMeX (Hydrological Cycle in the Mediterranean Experiment) Enhanced Observation Period (EOP) and lasts four years (2012-2015). In terms of hydrological modelling the objective is to set up models at the regional scale, while addressing small and generally ungauged catchments, which is the scale of interest for flooding risk assessment. Top-down and bottom-up approaches are combined and the models are used as "hypothesis testing" tools by coupling model development with data analyses, in order to incrementally evaluate the validity of model hypotheses. The paper first presents the rationale behind the experimental set up and the instrumentation itself. Second, we discuss the associated modelling strategy. Results illustrate the potential of the approach in advancing our understanding of flash flood processes at various scales.

  14. Multi-scale hydrometeorological observation and modelling for flash flood understanding

    NASA Astrophysics Data System (ADS)

    Braud, I.; Ayral, P.-A.; Bouvier, C.; Branger, F.; Delrieu, G.; Le Coz, J.; Nord, G.; Vandervaere, J.-P.; Anquetin, S.; Adamovic, M.; Andrieu, J.; Batiot, C.; Boudevillain, B.; Brunet, P.; Carreau, J.; Confoland, A.; Didon-Lescot, J.-F.; Domergue, J.-M.; Douvinet, J.; Dramais, G.; Freydier, R.; Gérard, S.; Huza, J.; Leblois, E.; Le Bourgeois, O.; Le Boursicaud, R.; Marchand, P.; Martin, P.; Nottale, L.; Patris, N.; Renard, B.; Seidel, J.-L.; Taupin, J.-D.; Vannier, O.; Vincendon, B.; Wijbrans, A.

    2014-09-01

    This paper presents a coupled observation and modelling strategy aiming at improving the understanding of processes triggering flash floods. This strategy is illustrated for the Mediterranean area using two French catchments (Gard and Ardèche) larger than 2000 km2. The approach is based on the monitoring of nested spatial scales: (1) the hillslope scale, where processes influencing the runoff generation and its concentration can be tackled; (2) the small to medium catchment scale (1-100 km2), where the impact of the network structure and of the spatial variability of rainfall, landscape and initial soil moisture can be quantified; (3) the larger scale (100-1000 km2), where the river routing and flooding processes become important. These observations are part of the HyMeX (HYdrological cycle in the Mediterranean EXperiment) enhanced observation period (EOP), which will last 4 years (2012-2015). In terms of hydrological modelling, the objective is to set up regional-scale models, while addressing small and generally ungauged catchments, which represent the scale of interest for flood risk assessment. Top-down and bottom-up approaches are combined and the models are used as "hypothesis testing" tools by coupling model development with data analyses in order to incrementally evaluate the validity of model hypotheses. The paper first presents the rationale behind the experimental set-up and the instrumentation itself. Second, we discuss the associated modelling strategy. Results illustrate the potential of the approach in advancing our understanding of flash flood processes on various scales.

  15. A multi-scale and model approach to estimate future tidal high water statistics in the southern German Bright

    NASA Astrophysics Data System (ADS)

    Hein, H.; Mai, S.; Mayer, B.; Pohlmann, T.; Barjenbruch, U.

    2012-04-01

    The interactions of tides, external surges, storm surges and waves with an additional role of the coastal bathymetry define the probability of extreme water levels at the coast. Probabilistic analysis and also process based numerical models allow the estimation of future states. From the physical point of view both, deterministic processes and stochastic residuals are the fundamentals of high water statistics. This study uses a so called model chain to reproduce historic statistics of tidal high water levels (Thw) as well as the prediction of future statistics high water levels. The results of the numerical models are post-processed by a stochastic analysis. Recent studies show, that for future extrapolation of extreme Thw nonstationary parametric approaches are required. With the presented methods a better prediction of time depended parameter sets seems possible. The investigation region of this study is the southern German Bright. The model-chain is the representation of a downscaling process, which starts with an emissions scenario. Regional atmospheric and ocean models refine the results of global climate models. The concept of downscaling was chosen to resolve coastal topography sufficiently. The North Sea and estuaries are modeled with the three-dimensional model HAMburg Shelf Ocean Model. The running time includes 150 years (1950 - 2100). Results of four different hindcast runs and also of one future prediction run are validated. Based on multi-scale analysis and the theory of entropy we analyze whether any significant periodicities are represented numerically. Results show that also hindcasting the climate of Thw with a model chain for the last 60 years is a challenging task. For example, an additional modeling activity must be the inclusion of tides into regional climate ocean models. It is found that the statistics of climate variables derived from model results differs from the statistics derived from measurements. E.g. there are considerable shifts in

  16. Multi-Scale Hydrometeorological Modeling, Land Data Assimilation and Parameter Estimation with the Land Information System

    NASA Technical Reports Server (NTRS)

    Peters-Lidard, Christa D.

    2011-01-01

    The Land Information System (LIS; http://lis.gsfc.nasa.gov) is a flexible land surface modeling framework that has been developed with the goal of integrating satellite-and ground-based observational data products and advanced land surface modeling techniques to produce optimal fields of land surface states and fluxes. As such, LIS represents a step towards the next generation land component of an integrated Earth system model. In recognition of LIS object-oriented software design, use and impact in the land surface and hydrometeorological modeling community, the LIS software was selected as a co-winner of NASA?s 2005 Software of the Year award.LIS facilitates the integration of observations from Earth-observing systems and predictions and forecasts from Earth System and Earth science models into the decision-making processes of partnering agency and national organizations. Due to its flexible software design, LIS can serve both as a Problem Solving Environment (PSE) for hydrologic research to enable accurate global water and energy cycle predictions, and as a Decision Support System (DSS) to generate useful information for application areas including disaster management, water resources management, agricultural management, numerical weather prediction, air quality and military mobility assessment. LIS has e volved from two earlier efforts -- North American Land Data Assimilation System (NLDAS) and Global Land Data Assimilation System (GLDAS) that focused primarily on improving numerical weather prediction skills by improving the characterization of the land surface conditions. Both of GLDAS and NLDAS now use specific configurations of the LIS software in their current implementations.In addition, LIS was recently transitioned into operations at the US Air Force Weather Agency (AFWA) to ultimately replace their Agricultural Meteorology (AGRMET) system, and is also used routinely by NOAA's National Centers for Environmental Prediction (NCEP)/Environmental Modeling

  17. Multi-Scale Hydrometeorological Modeling, Land Data Assimilation and Parameter Estimation with the Land Information System

    NASA Technical Reports Server (NTRS)

    Peters-Lidard, Christa D.; Kumar, Sujay V.; Santanello, Joseph A., Jr.; Reichle, Rolf H.

    2009-01-01

    The Land Information System (LIS; http://lis.gsfc.nasa.gov; Kumar et al., 2006; Peters- Lidard et al.,2007) is a flexible land surface modeling framework that has been developed with the goal of integrating satellite- and ground-based observational data products and advanced land surface modeling techniques to produce optimal fields of land surface states and fluxes. As such, LIS represents a step towards the next generation land component of an integrated Earth system model. In recognition of LIS object-oriented software design, use and impact in the land surface and hydrometeorological modeling community, the LIS software was selected ase co-winner of NASA's 2005 Software of the Year award. LIS facilitates the integration of observations from Earth-observing systems and predictions and forecasts from Earth System and Earth science models into the decision-making processes of partnering agency and national organizations. Due to its flexible software design, LIS can serve both as a Problem Solving Environment (PSE) for hydrologic research to enable accurate global water and energy cycle predictions, and as a Decision Support System (DSS) to generate useful information for application areas including disaster management, water resources management, agricultural management, numerical weather prediction, air quality and military mobility assessment. LIS has evolved from two earlier efforts North American Land Data Assimilation System (NLDAS; Mitchell et al. 2004) and Global Land Data Assimilation System (GLDAS; Rodell al. 2004) that focused primarily on improving numerical weather prediction skills by improving the characterization of the land surface conditions. Both of GLDAS and NLDAS now use specific configurations of the LIS software in their current implementations. In addition, LIS was recently transitioned into operations at the US Air Force Weather Agency (AFWA) to ultimately replace their Agricultural Meteorology (AGRMET) system, and is also used routinely by

  18. Basilar membrane and reticular lamina motion in a multi-scale finite element model of the mouse cochlea

    NASA Astrophysics Data System (ADS)

    Soons, Joris; Dirckx, Joris; Steele, Charles; Puria, Sunil

    2015-12-01

    A multi-scale finite element (FE) model of the mouse cochlea, based on its anatomy and material properties is presented. The important feature in the model is a lattice of 400 Y-shaped structures in the longitudinal direction, each formed by Deiters cells, phalangeal processes and outer hair cells (OHC). OHC somatic motility is modeled by an expansion force proportional to the shear on the stereocilia, which in turn is proportional to the pressure difference between the scala vestibule and scala tympani. Basilar membrane (BM) and reticular lamina (RL) velocity compare qualitatively very well with recent in vivo measurements in guinea pig [2]. Compared to the BM, the RL is shown to have higher amplification and a shift to higher frequencies. This comes naturally from the realistic Y-shaped cell organization without tectorial membrane tuning.

  19. Posterior predictive modeling using multi-scale stochastic inverse parameter estimates.

    SciTech Connect

    Waanders, Bart Van Bloemen; Marzouk, Youssef M.; Ray, Jaideep; McKenna, Sean Andrew

    2010-12-01

    Multi-scale binary permeability field estimation from static and dynamic data is completed using Markov Chain Monte Carlo (MCMC) sampling. The binary permeability field is defined as high permeability inclusions within a lower permeability matrix. Static data are obtained as measurements of permeability with support consistent to the coarse scale discretization. Dynamic data are advective travel times along streamlines calculated through a fine-scale field and averaged for each observation point at the coarse scale. Parameters estimated at the coarse scale (30 x 20 grid) are the spatially varying proportion of the high permeability phase and the inclusion length and aspect ratio of the high permeability inclusions. From the non-parametric, posterior distributions estimated for these parameters, a recently developed sub-grid algorithm is employed to create an ensemble of realizations representing the fine-scale (3000 x 2000), binary permeability field. Each fine-scale ensemble member is instantiated by convolution of an uncorrelated multiGaussian random field with a Gaussian kernel defined by the estimated inclusion length and aspect ratio. Since the multiGaussian random field is itself a realization of a stochastic process, the procedure for generating fine-scale binary permeability field realizations is also stochastic. Two different methods are hypothesized to perform posterior predictive tests. Different mechanisms for combining multi Gaussian random fields with kernels defined from the MCMC sampling are examined. Posterior predictive accuracy of the estimated parameters is assessed against a simulated ground truth for predictions at both the coarse scale (effective permeabilities) and at the fine scale (advective travel time distributions). The two techniques for conducting posterior predictive tests are compared by their ability to recover the static and dynamic data. The skill of the inference and the method for generating fine-scale binary permeability

  20. Test-particle simulation in three-dimensional multi-scale RMHD model of turbulence

    NASA Astrophysics Data System (ADS)

    Dalena, S.; Rappazzo, A. F.; Matthaeus, W. H.

    2012-12-01

    The acceleration of charged particles is relevant in the solar corona over a range of scales and energies. Acceleration can occur in large events like flares, but also in smaller events characterized by dynamical activity near current sheets. In order to gain some insights into the complex scenario of coronal charged particle acceleration, we investigate the properties of acceleration using 3D MHD simulation augmented by a test-particle approach. This provides a useful bridge between the large-scale macroscopic MHD and a more realistic particle kinetic physics description. Numerical experiments are performed using turbulent magnetic and electric fields obtained from direct solutions of Reduced MHD equations, which are well suited for a plasma embedded in a strong axial magnetic field, as in the case of coronal loops. Indeed a coronal loop is a closed magnetic structure threaded by a strong axial field, with the footpoints rooted in the photosphere. This makes it a strongly anisotropic system. A multi-box, multi-scale technique is used to solve the equation of motion for protons. This methods allow us to resolve all the length present in the system, namely from the outer scale of the order of 4000km to the ion skin depth of the order of a meter. This new technique is useful to identify the mechanisms that, acting on different scales, are responsible for acceleration to high energies of a small fraction of the particles in the coronal plasma. We report results that show acceleration at different stages over a broad range of time, length and energy scales.

  1. MULTI-SCALE MODELING AND APPROXIMATION ASSISTED OPTIMIZATION OF BARE TUBE HEAT EXCHANGERS

    SciTech Connect

    Bacellar, Daniel; Ling, Jiazhen; Aute, Vikrant; Radermacher, Reinhard; Abdelaziz, Omar

    2014-01-01

    Air-to-refrigerant heat exchangers are very common in air-conditioning, heat pump and refrigeration applications. In these heat exchangers, there is a great benefit in terms of size, weight, refrigerant charge and heat transfer coefficient, by moving from conventional channel sizes (~ 9mm) to smaller channel sizes (< 5mm). This work investigates new designs for air-to-refrigerant heat exchangers with tube outer diameter ranging from 0.5 to 2.0mm. The goal of this research is to develop and optimize the design of these heat exchangers and compare their performance with existing state of the art designs. The air-side performance of various tube bundle configurations are analyzed using a Parallel Parameterized CFD (PPCFD) technique. PPCFD allows for fast-parametric CFD analyses of various geometries with topology change. Approximation techniques drastically reduce the number of CFD evaluations required during optimization. Maximum Entropy Design method is used for sampling and Kriging method is used for metamodeling. Metamodels are developed for the air-side heat transfer coefficients and pressure drop as a function of tube-bundle dimensions and air velocity. The metamodels are then integrated with an air-to-refrigerant heat exchanger design code. This integration allows a multi-scale analysis of air-side performance heat exchangers including air-to-refrigerant heat transfer and phase change. Overall optimization is carried out using a multi-objective genetic algorithm. The optimal designs found can exhibit 50 percent size reduction, 75 percent decrease in air side pressure drop and doubled air heat transfer coefficients compared to a high performance compact micro channel heat exchanger with same capacity and flow rates.

  2. Predicting Species Distributions Using Record Centre Data: Multi-Scale Modelling of Habitat Suitability for Bat Roosts

    PubMed Central

    Bellamy, Chloe; Altringham, John

    2015-01-01

    Conservation increasingly operates at the landscape scale. For this to be effective, we need landscape scale information on species distributions and the environmental factors that underpin them. Species records are becoming increasingly available via data centres and online portals, but they are often patchy and biased. We demonstrate how such data can yield useful habitat suitability models, using bat roost records as an example. We analysed the effects of environmental variables at eight spatial scales (500 m – 6 km) on roost selection by eight bat species (Pipistrellus pipistrellus, P. pygmaeus, Nyctalus noctula, Myotis mystacinus, M. brandtii, M. nattereri, M. daubentonii, and Plecotus auritus) using the presence-only modelling software MaxEnt. Modelling was carried out on a selection of 418 data centre roost records from the Lake District National Park, UK. Target group pseudoabsences were selected to reduce the impact of sampling bias. Multi-scale models, combining variables measured at their best performing spatial scales, were used to predict roosting habitat suitability, yielding models with useful predictive abilities. Small areas of deciduous woodland consistently increased roosting habitat suitability, but other habitat associations varied between species and scales. Pipistrellus were positively related to built environments at small scales, and depended on large-scale woodland availability. The other, more specialist, species were highly sensitive to human-altered landscapes, avoiding even small rural towns. The strength of many relationships at large scales suggests that bats are sensitive to habitat modifications far from the roost itself. The fine resolution, large extent maps will aid targeted decision-making by conservationists and planners. We have made available an ArcGIS toolbox that automates the production of multi-scale variables, to facilitate the application of our methods to other taxa and locations. Habitat suitability modelling has

  3. Multi-scale diffuse interface modeling of multi-component two-phase flow with partial miscibility

    NASA Astrophysics Data System (ADS)

    Kou, Jisheng; Sun, Shuyu

    2016-08-01

    In this paper, we introduce a diffuse interface model to simulate multi-component two-phase flow with partial miscibility based on a realistic equation of state (e.g. Peng-Robinson equation of state). Because of partial miscibility, thermodynamic relations are used to model not only interfacial properties but also bulk properties, including density, composition, pressure, and realistic viscosity. As far as we know, this effort is the first time to use diffuse interface modeling based on equation of state for modeling of multi-component two-phase flow with partial miscibility. In numerical simulation, the key issue is to resolve the high contrast of scales from the microscopic interface composition to macroscale bulk fluid motion since the interface has a nanoscale thickness only. To efficiently solve this challenging problem, we develop a multi-scale simulation method. At the microscopic scale, we deduce a reduced interfacial equation under reasonable assumptions, and then we propose a formulation of capillary pressure, which is consistent with macroscale flow equations. Moreover, we show that Young-Laplace equation is an approximation of this capillarity formulation, and this formulation is also consistent with the concept of Tolman length, which is a correction of Young-Laplace equation. At the macroscopical scale, the interfaces are treated as discontinuous surfaces separating two phases of fluids. Our approach differs from conventional sharp-interface two-phase flow model in that we use the capillary pressure directly instead of a combination of surface tension and Young-Laplace equation because capillarity can be calculated from our proposed capillarity formulation. A compatible condition is also derived for the pressure in flow equations. Furthermore, based on the proposed capillarity formulation, we design an efficient numerical method for directly computing the capillary pressure between two fluids composed of multiple components. Finally, numerical tests

  4. Multi-scale diffuse interface modeling of multi-component two-phase flow with partial miscibility

    SciTech Connect

    Kou, Jisheng; Sun, Shuyu

    2016-08-01

    In this paper, we introduce a diffuse interface model to simulate multi-component two-phase flow with partial miscibility based on a realistic equation of state (e.g. Peng–Robinson equation of state). Because of partial miscibility, thermodynamic relations are used to model not only interfacial properties but also bulk properties, including density, composition, pressure, and realistic viscosity. As far as we know, this effort is the first time to use diffuse interface modeling based on equation of state for modeling of multi-component two-phase flow with partial miscibility. In numerical simulation, the key issue is to resolve the high contrast of scales from the microscopic interface composition to macroscale bulk fluid motion since the interface has a nanoscale thickness only. To efficiently solve this challenging problem, we develop a multi-scale simulation method. At the microscopic scale, we deduce a reduced interfacial equation under reasonable assumptions, and then we propose a formulation of capillary pressure, which is consistent with macroscale flow equations. Moreover, we show that Young–Laplace equation is an approximation of this capillarity formulation, and this formulation is also consistent with the concept of Tolman length, which is a correction of Young–Laplace equation. At the macroscopical scale, the interfaces are treated as discontinuous surfaces separating two phases of fluids. Our approach differs from conventional sharp-interface two-phase flow model in that we use the capillary pressure directly instead of a combination of surface tension and Young–Laplace equation because capillarity can be calculated from our proposed capillarity formulation. A compatible condition is also derived for the pressure in flow equations. Furthermore, based on the proposed capillarity formulation, we design an efficient numerical method for directly computing the capillary pressure between two fluids composed of multiple components. Finally, numerical

  5. Multi-scale modeling of microstructure dependent intergranular brittle fracture using a quantitative phase-field based method

    DOE PAGES

    Chakraborty, Pritam; Zhang, Yongfeng; Tonks, Michael R.

    2015-12-07

    In this study, the fracture behavior of brittle materials is strongly influenced by their underlying microstructure that needs explicit consideration for accurate prediction of fracture properties and the associated scatter. In this work, a hierarchical multi-scale approach is pursued to model microstructure sensitive brittle fracture. A quantitative phase-field based fracture model is utilized to capture the complex crack growth behavior in the microstructure and the related parameters are calibrated from lower length scale atomistic simulations instead of engineering scale experimental data. The workability of this approach is demonstrated by performing porosity dependent intergranular fracture simulations in UO2 and comparing themore » predictions with experiments.« less

  6. Multi-scale brain networks.

    PubMed

    Betzel, Richard F; Bassett, Danielle S

    2016-11-11

    The network architecture of the human brain has become a feature of increasing interest to the neuroscientific community, largely because of its potential to illuminate human cognition, its variation over development and aging, and its alteration in disease or injury. Traditional tools and approaches to study this architecture have largely focused on single scales-of topology, time, and space. Expanding beyond this narrow view, we focus this review on pertinent questions and novel methodological advances for the multi-scale brain. We separate our exposition into content related to multi-scale topological structure, multi-scale temporal structure, and multi-scale spatial structure. In each case, we recount empirical evidence for such structures, survey network-based methodological approaches to reveal these structures, and outline current frontiers and open questions. Although predominantly peppered with examples from human neuroimaging, we hope that this account will offer an accessible guide to any neuroscientist aiming to measure, characterize, and understand the full richness of the brain's multiscale network structure-irrespective of species, imaging modality, or spatial resolution.

  7. A Unified Multi-scale Model for Cross-Scale Evaluation and Integration of Hydrological and Biogeochemical Processes

    NASA Astrophysics Data System (ADS)

    Liu, C.; Yang, X.; Bailey, V. L.; Bond-Lamberty, B. P.; Hinkle, C.

    2013-12-01

    Mathematical representations of hydrological and biogeochemical processes in soil, plant, aquatic, and atmospheric systems vary with scale. Process-rich models are typically used to describe hydrological and biogeochemical processes at the pore and small scales, while empirical, correlation approaches are often used at the watershed and regional scales. A major challenge for multi-scale modeling is that water flow, biogeochemical processes, and reactive transport are described using different physical laws and/or expressions at the different scales. For example, the flow is governed by the Navier-Stokes equations at the pore-scale in soils, by the Darcy law in soil columns and aquifer, and by the Navier-Stokes equations again in open water bodies (ponds, lake, river) and atmosphere surface layer. This research explores whether the physical laws at the different scales and in different physical domains can be unified to form a unified multi-scale model (UMSM) to systematically investigate the cross-scale, cross-domain behavior of fundamental processes at different scales. This presentation will discuss our research on the concept, mathematical equations, and numerical execution of the UMSM. Three-dimensional, multi-scale hydrological processes at the Disney Wilderness Preservation (DWP) site, Florida will be used as an example for demonstrating the application of the UMSM. In this research, the UMSM was used to simulate hydrological processes in rooting zones at the pore and small scales including water migration in soils under saturated and unsaturated conditions, root-induced hydrological redistribution, and role of rooting zone biogeochemical properties (e.g., root exudates and microbial mucilage) on water storage and wetting/draining. The small scale simulation results were used to estimate effective water retention properties in soil columns that were superimposed on the bulk soil water retention properties at the DWP site. The UMSM parameterized from smaller

  8. A multi-scale GIS and hydrodynamic modelling approach to fish passage assessment: Clarence and Shoalhaven Rivers, NSW Australia

    NASA Astrophysics Data System (ADS)

    Bonetti, Rita M.; Reinfelds, Ivars V.; Butler, Gavin L.; Walsh, Chris T.; Broderick, Tony J.; Chisholm, Laurie A.

    2016-05-01

    Natural barriers such as waterfalls, cascades, rapids and riffles limit the dispersal and in-stream range of migratory fish, yet little is known of the interplay between these gradient dependent landforms, their hydraulic characteristics and flow rates that facilitate fish passage. The resurgence of dam construction in numerous river basins world-wide provides impetus to the development of robust techniques for assessment of the effects of downstream flow regime changes on natural fish passage barriers and associated consequences as to the length of rivers available to migratory species. This paper outlines a multi-scale technique for quantifying the relative magnitude of natural fish passage barriers in river systems and flow rates that facilitate passage by fish. First, a GIS-based approach is used to quantify channel gradients for the length of river or reach under investigation from a high resolution DEM, setting the magnitude of identified passage barriers in a longer context (tens to hundreds of km). Second, LiDAR, topographic and bathymetric survey-based hydrodynamic modelling is used to assess flow rates that can be regarded as facilitating passage across specific barriers identified by the river to reach scale gradient analysis. Examples of multi-scale approaches to fish passage assessment for flood-flow and low-flow passage issues are provided from the Clarence and Shoalhaven Rivers, NSW, Australia. In these river systems, passive acoustic telemetry data on actual movements and migrations by Australian bass (Macquaria novemaculeata) provide a means of validating modelled assessments of flow rates associated with successful fish passage across natural barriers. Analysis of actual fish movements across passage barriers in these river systems indicates that two dimensional hydraulic modelling can usefully quantify flow rates associated with the facilitation of fish passage across natural barriers by a majority of individual fishes for use in management

  9. Modeling Low-Flow Sensitivity to Climate Variability and Forest Harvesting in the Willamette Basin: A Multi-scale Approach.

    NASA Astrophysics Data System (ADS)

    Choate, J.; Tague, C.; Grant, G.

    2002-12-01

    In the mountainous region of the Pacific Northwest, underlying geologic and vegetation patterns, forest management practices and climate regimes at different elevations mediate the response of low flows occurring in late summer. Low-stream flow conditions, occurring during the warm, dry summers are critical to river ecosystem function and crucial to many aquatic and riparian species life cycles as well as human uses of streams. Understanding the different controls on low flow variability in this region requires a multi-scale perspective. This particular study is part of a larger strategy designed to use both empirical analysis and physically based, hydro-ecological modeling to disentangle the role that climate, geology and forest harvesting play in controlling low flows in 1st to 5th order watersheds within the Willamette basin. Our empirical analysis of summer low flow for a range of streams has shown that summer, unit-area discharge volumes are significantly lower for streams in the geologically distinct and low elevation Western Cascade versus High Cascade areas. This empirical analysis outlines large-scale regional variability. To assess and compare this with smaller scale variability, we use the RHESSys model (Regional Hydro-Ecologic Simulation System) to assess low flow behavior for small 1st order streams within the Western Cascade region. The goal is to examine low flow variability due to both climate and forest harvesting and recovery and place this in the context of regional scale analysis. We use multiple simulations to predict low flow volumes under cut and uncut conditions for wet/dry and warm/cool climate scenarios. Future work will replicate this study to examine 1st order watershed sensitivity within the contrasting High Cascade geologic region. The combined multi-scale empirical and modeling approach will then be used to provide a more comprehensive assessment of low flow patterns and sensitivity within this region.

  10. Directional Multi-scale Modeling of High-Resolution Computed Tomography (HRCT) Lung Images for Diffuse Lung Disease Classification

    NASA Astrophysics Data System (ADS)

    Vo, Kiet T.; Sowmya, Arcot

    A directional multi-scale modeling scheme based on wavelet and contourlet transforms is employed to describe HRCT lung image textures for classifying four diffuse lung disease patterns: normal, emphysema, ground glass opacity (GGO) and honey-combing. Generalized Gaussian density parameters are used to represent the detail sub-band features obtained by wavelet and contourlet transforms. In addition, support vector machines (SVMs) with excellent performance in a variety of pattern classification problems are used as classifier. The method is tested on a collection of 89 slices from 38 patients, each slice of size 512x512, 16 bits/pixel in DICOM format. The dataset contains 70,000 ROIs of those slices marked by experienced radiologists. We employ this technique at different wavelet and contourlet transform scales for diffuse lung disease classification. The technique presented here has best overall sensitivity 93.40% and specificity 98.40%.

  11. Modeling and simulation of multi-physics multi-scale transport phenomenain bio-medical applications

    NASA Astrophysics Data System (ADS)

    Kenjereš, Saša

    2014-08-01

    We present a short overview of some of our most recent work that combines the mathematical modeling, advanced computer simulations and state-of-the-art experimental techniques of physical transport phenomena in various bio-medical applications. In the first example, we tackle predictions of complex blood flow patterns in the patient-specific vascular system (carotid artery bifurcation) and transfer of the so-called "bad" cholesterol (low-density lipoprotein, LDL) within the multi-layered artery wall. This two-way coupling between the blood flow and corresponding mass transfer of LDL within the artery wall is essential for predictions of regions where atherosclerosis can develop. It is demonstrated that a recently developed mathematical model, which takes into account the complex multi-layer arterial-wall structure, produced LDL profiles within the artery wall in good agreement with in-vivo experiments in rabbits, and it can be used for predictions of locations where the initial stage of development of atherosclerosis may take place. The second example includes a combination of pulsating blood flow and medical drug delivery and deposition controlled by external magnetic field gradients in the patient specific carotid artery bifurcation. The results of numerical simulations are compared with own PIV (Particle Image Velocimetry) and MRI (Magnetic Resonance Imaging) in the PDMS (silicon-based organic polymer) phantom. A very good agreement between simulations and experiments is obtained for different stages of the pulsating cycle. Application of the magnetic drug targeting resulted in an increase of up to ten fold in the efficiency of local deposition of the medical drug at desired locations. Finally, the LES (Large Eddy Simulation) of the aerosol distribution within the human respiratory system that includes up to eight bronchial generations is performed. A very good agreement between simulations and MRV (Magnetic Resonance Velocimetry) measurements is obtained

  12. The NASA-Goddard Multi-Scale Modeling Framework - Land Information System: Global Land/atmosphere Interaction with Resolved Convection

    NASA Technical Reports Server (NTRS)

    Mohr, Karen Irene; Tao, Wei-Kuo; Chern, Jiun-Dar; Kumar, Sujay V.; Peters-Lidard, Christa D.

    2013-01-01

    The present generation of general circulation models (GCM) use parameterized cumulus schemes and run at hydrostatic grid resolutions. To improve the representation of cloud-scale moist processes and landeatmosphere interactions, a global, Multi-scale Modeling Framework (MMF) coupled to the Land Information System (LIS) has been developed at NASA-Goddard Space Flight Center. The MMFeLIS has three components, a finite-volume (fv) GCM (Goddard Earth Observing System Ver. 4, GEOS-4), a 2D cloud-resolving model (Goddard Cumulus Ensemble, GCE), and the LIS, representing the large-scale atmospheric circulation, cloud processes, and land surface processes, respectively. The non-hydrostatic GCE model replaces the single-column cumulus parameterization of fvGCM. The model grid is composed of an array of fvGCM gridcells each with a series of embedded GCE models. A horizontal coupling strategy, GCE4fvGCM4Coupler4LIS, offered significant computational efficiency, with the scalability and I/O capabilities of LIS permitting landeatmosphere interactions at cloud-scale. Global simulations of 2007e2008 and comparisons to observations and reanalysis products were conducted. Using two different versions of the same land surface model but the same initial conditions, divergence in regional, synoptic-scale surface pressure patterns emerged within two weeks. The sensitivity of largescale circulations to land surface model physics revealed significant functional value to using a scalable, multi-model land surface modeling system in global weather and climate prediction.

  13. A Multi-Scale Model of the Circulatory System for the Study of Left Ventricular Assist Devices

    NASA Astrophysics Data System (ADS)

    Gohean, J. R.; Moser, R. D.; Bazilevs, Y.; Hughes, T. J. R.

    2006-11-01

    A computer model of the cardiovascular system has been developed to study the hemodynamic effects of a non-pulsatile axial flow left ventricular assist device (LVAD). The model is multi-scale and consists of a distributed quasi-one-dimensional arterial tree, based on integrated Navier-Stokes with a pressure/area state equation representing the compliance of the arteries; and lumped parameter models for the systemic return, pulmonary circulation, coronary circulation, and heart. Physiologically consistent aortic pressure and flow histories have been obtained by including a dynamic aortic valve model that allows back-flow by representing leaflet motion. In addition, a three-dimensional finite element model of the aorta with nonlinear elastic arterial walls can be integrated with the quasi-one-dimensional and lumped parameter models, with the lower fidelity models providing boundary conditions for the detailed model. The three dimensional model allows investigation of the detailed flow characteristics induced by the LVAD. The effect of an LVAD and its implant configuration on the hemodynamics of the cardiovascular system and coronary perfusion are studied for various patient conditions and levels of assist.

  14. Development of high-resolution multi-scale modelling system for simulation of coastal-fluvial urban flooding

    NASA Astrophysics Data System (ADS)

    Comer, Joanne; Indiana Olbert, Agnieszka; Nash, Stephen; Hartnett, Michael

    2017-02-01

    Urban developments in coastal zones are often exposed to natural hazards such as flooding. In this research, a state-of-the-art, multi-scale nested flood (MSN_Flood) model is applied to simulate complex coastal-fluvial urban flooding due to combined effects of tides, surges and river discharges. Cork city on Ireland's southwest coast is a study case. The flood modelling system comprises a cascade of four dynamically linked models that resolve the hydrodynamics of Cork Harbour and/or its sub-region at four scales: 90, 30, 6 and 2 m. Results demonstrate that the internalization of the nested boundary through the use of ghost cells combined with a tailored adaptive interpolation technique creates a highly dynamic moving boundary that permits flooding and drying of the nested boundary. This novel feature of MSN_Flood provides a high degree of choice regarding the location of the boundaries to the nested domain and therefore flexibility in model application. The nested MSN_Flood model through dynamic downscaling facilitates significant improvements in accuracy of model output without incurring the computational expense of high spatial resolution over the entire model domain. The urban flood model provides full characteristics of water levels and flow regimes necessary for flood hazard identification and flood risk assessment.

  15. Computational Modeling of Multi-Scale Material Features in Cement Paste - An Overview

    DTIC Science & Technology

    2015-05-25

    from nanoscale material features through material chemistry modeling via molecular dynamics (MD); modeling of complete three-dimensional virtual...material features through material chemistry modeling via molecular dynamics (MD); modeling of complete three-dimensional virtual microstructure...including the evolution of microstructure due to hydration of cementitious materials are briefly highlighted. Material chemistry modeling discussions from

  16. A Micromechanical Unit Cell Model of 2 × 2 Twill Woven Fabric Textile Composite for Multi Scale Analysis

    NASA Astrophysics Data System (ADS)

    Dixit, A.; Mali, H. S.; Misra, R. K.

    2014-04-01

    Woven fabric based composite materials are being considered for potential structural applications in automotive and aircraft industries due to their better out of plane strength, stiffness and toughness properties than ordinary composite laminates. This paper presents the micromechanical unit cell model of 2 × 2 twill woven fabric textile composite for the estimation of in-plane elastic properties. Modelling of unit cell and its analysis for this new model is developed by using open source coded tool TexGen and finite element software, ABAQUS® respectively. The predicted values are in good agreement with the experimental results reported in literature. To ascertain the effectiveness of the developed model parametric studies have also been conducted on the predicted elastic properties in order to investigate the effects of various geometric parameters such as yarn spacing, fabric thickness, yarn width and fibre volume fraction. The scope of altering weave pattern and yarn characteristics is facilitated in this developed model. Further this model can be implemented for the multi-scale micro/macro-mechanical analysis for the calculation of strength and stiffness of laminates structure made of 2 × 2 twill composite.

  17. A multi-scale continuum model of skeletal muscle mechanics predicting force enhancement based on actin-titin interaction.

    PubMed

    Heidlauf, Thomas; Klotz, Thomas; Rode, Christian; Altan, Ekin; Bleiler, Christian; Siebert, Tobias; Röhrle, Oliver

    2016-12-01

    Although recent research emphasises the possible role of titin in skeletal muscle force enhancement, this property is commonly ignored in current computational models. This work presents the first biophysically based continuum-mechanical model of skeletal muscle that considers, in addition to actin-myosin interactions, force enhancement based on actin-titin interactions. During activation, titin attaches to actin filaments, which results in a significant reduction in titin's free molecular spring length and therefore results in increased titin forces during a subsequent stretch. The mechanical behaviour of titin is included on the microscopic half-sarcomere level of a multi-scale chemo-electro-mechanical muscle model, which is based on the classic sliding-filament and cross-bridge theories. In addition to titin stress contributions in the muscle fibre direction, the continuum-mechanical constitutive relation accounts for geometrically motivated, titin-induced stresses acting in the muscle's cross-fibre directions. Representative simulations of active stretches under maximal and submaximal activation levels predict realistic magnitudes of force enhancement in fibre direction. For example, stretching the model by 20 % from optimal length increased the isometric force at the target length by about 30 %. Predicted titin-induced stresses in the muscle's cross-fibre directions are rather insignificant. Including the presented development in future continuum-mechanical models of muscle function in dynamic situations will lead to more accurate model predictions during and after lengthening contractions.

  18. Impact of spatial data resolution on simulated catchment water balances and model performance of the multi-scale TOPLATS model

    NASA Astrophysics Data System (ADS)

    Bormann, H.

    2005-10-01

    This paper analyses the effect of spatial input data resolution on the simulated water balances and flow components using the multi-scale hydrological model TOPLATS. A data set of 25m resolution of the central German Dill catchment (693 km2 is used for investigation. After an aggregation of digital elevation model, soil map and land use classification to 50 m, 75 m, 100 m, 150 m, 200 m, 300 m, 500 m, 1000 m and 2000 m, water balances and water flow components are calculated for the entire Dill catchment as well as for 3 subcatchments without any recalibration. The study shows that both model performance measures as well as simulated water balances almost remain constant for most of the aggregation steps for all investigated catchments. Slight differences occur for single catchments at the resolution of 50-500 m (e.g. 0-3% for annual stream flow), significant differences at the resolution of 1000 m and 2000 m (e.g. 2-12% for annual stream flow). These differences can be explained by the fact that the statistics of certain input data (land use data in particular as well as soil physical characteristics) changes significantly at these spatial resolutions, too. The impact of smoothing the relief by aggregation occurs continuously but is not reflected by the simulation results. To study the effect of aggregation of land use data in detail, three different land use scenarios are aggregated which were generated aiming on economic optimisation at different field sizes (0.5 ha, 1.5 ha and 5.0 ha). The changes induced by aggregation of these land use scenarios are comparable with respect to catchment water balances compared to the current land use. A correlation analysis only in some cases reveals high correlation between changes in both input data and in simulation results for all catchments and land use scenarios combinations (e.g. evapotranspiration is correlated to land use, runoff generation is correlated to soil properties). Predominantly the correlation between

  19. Hierarchical multi-scale approach to validation and uncertainty quantification of hyper-spectral image modeling

    NASA Astrophysics Data System (ADS)

    Engel, Dave W.; Reichardt, Thomas A.; Kulp, Thomas J.; Graff, David L.; Thompson, Sandra E.

    2016-05-01

    Validating predictive models and quantifying uncertainties inherent in the modeling process is a critical component of the HARD Solids Venture program [1]. Our current research focuses on validating physics-based models predicting the optical properties of solid materials for arbitrary surface morphologies and characterizing the uncertainties in these models. We employ a systematic and hierarchical approach by designing physical experiments and comparing the experimental results with the outputs of computational predictive models. We illustrate this approach through an example comparing a micro-scale forward model to an idealized solid-material system and then propagating the results through a system model to the sensor level. Our efforts should enhance detection reliability of the hyper-spectral imaging technique and the confidence in model utilization and model outputs by users and stakeholders.

  20. Hierarchical Multi-Scale Approach To Validation and Uncertainty Quantification of Hyper-Spectral Image Modeling

    SciTech Connect

    Engel, David W.; Reichardt, Thomas A.; Kulp, Thomas J.; Graff, David; Thompson, Sandra E.

    2016-09-17

    Validating predictive models and quantifying uncertainties inherent in the modeling process is a critical component of the HARD Solids Venture program [1]. Our current research focuses on validating physics-based models predicting the optical properties of solid materials for arbitrary surface morphologies and characterizing the uncertainties in these models. We employ a systematic and hierarchical approach by designing physical experiments and comparing the experimental results with the outputs of computational predictive models. We illustrate this approach through an example comparing a micro-scale forward model to an idealized solid-material system and then propagating the results through a system model to the sensor level. Our efforts should enhance detection reliability of the hyper-spectral imaging technique and the confidence in model utilization and model outputs by users and stakeholders.

  1. A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins.

    PubMed

    Suryawanshi, Gajendra W; Hoffmann, Alexander

    2015-12-07

    Human immunodeficiency virus-1 (HIV-1) employs accessory proteins to evade innate immune responses by neutralizing the anti-viral activity of host restriction factors. Apolipoprotein B mRNA-editing enzyme 3G (APOBEC3G, A3G) and bone marrow stromal cell antigen 2 (BST2) are host resistance factors that potentially inhibit HIV-1 infection. BST2 reduces viral production by tethering budding HIV-1 particles to virus producing cells, while A3G inhibits the reverse transcription (RT) process and induces viral genome hypermutation through cytidine deamination, generating fewer replication competent progeny virus. Two HIV-1 proteins counter these cellular restriction factors: Vpu, which reduces surface BST2, and Vif, which degrades cellular A3G. The contest between these host and viral proteins influences whether HIV-1 infection is established and progresses towards AIDS. In this work, we present an age-structured multi-scale viral dynamics model of in vivo HIV-1 infection. We integrated the intracellular dynamics of anti-viral activity of the host factors and their neutralization by HIV-1 accessory proteins into the virus/cell population dynamics model. We calculate the basic reproductive ratio (Ro) as a function of host-viral protein interaction coefficients, and numerically simulated the multi-scale model to understand HIV-1 dynamics following host factor-induced perturbations. We found that reducing the influence of Vpu triggers a drop in Ro, revealing the impact of BST2 on viral infection control. Reducing Vif׳s effect reveals the restrictive efficacy of A3G in blocking RT and in inducing lethal hypermutations, however, neither of these factors alone is sufficient to fully restrict HIV-1 infection. Interestingly, our model further predicts that BST2 and A3G function synergistically, and delineates their relative contribution in limiting HIV-1 infection and disease progression. We provide a robust modeling framework for devising novel combination therapies that target

  2. A Comprehensive, Multi-Scale Dynamical Model of ErbB Receptor Signal Transduction in Human Mammary Epithelial Cells

    PubMed Central

    Helikar, Tomáš; Kochi, Naomi; Kowal, Bryan; Dimri, Manjari; Naramura, Mayumi; Raja, Srikumar M.; Band, Vimla; Band, Hamid; Rogers, Jim A.

    2013-01-01

    The non-receptor tyrosine kinase Src and receptor tyrosine kinase epidermal growth factor receptor (EGFR/ErbB1) have been established as collaborators in cellular signaling and their combined dysregulation plays key roles in human cancers, including breast cancer. In part due to the complexity of the biochemical network associated with the regulation of these proteins as well as their cellular functions, the role of Src in EGFR regulation remains unclear. Herein we present a new comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells. This model, constructed manually from published biochemical literature, consists of 245 nodes representing proteins and their post-translational modifications sites, and over 1,000 biochemical interactions. Using computer simulations of the model, we find it is able to reproduce a number of cellular phenomena. Furthermore, the model predicts that overexpression of Src results in increased endocytosis of EGFR in the absence/low amount of the epidermal growth factor (EGF). Our subsequent laboratory experiments also suggest increased internalization of EGFR upon Src overexpression under EGF-deprived conditions, further supporting this model-generated hypothesis. PMID:23637902

  3. Interacting price model and fluctuation behavior analysis from Lempel-Ziv complexity and multi-scale weighted-permutation entropy

    NASA Astrophysics Data System (ADS)

    Li, Rui; Wang, Jun

    2016-01-01

    A financial price model is developed based on the voter interacting system in this work. The Lempel-Ziv complexity is introduced to analyze the complex behaviors of the stock market. Some stock market stylized facts including fat tails, absence of autocorrelation and volatility clustering are investigated for the proposed price model firstly. Then the complexity of fluctuation behaviors of the real stock markets and the proposed price model are mainly explored by Lempel-Ziv complexity (LZC) analysis and multi-scale weighted-permutation entropy (MWPE) analysis. A series of LZC analyses of the returns and the absolute returns of daily closing prices and moving average prices are performed. Moreover, the complexity of the returns, the absolute returns and their corresponding intrinsic mode functions (IMFs) derived from the empirical mode decomposition (EMD) with MWPE is also investigated. The numerical empirical study shows similar statistical and complex behaviors between the proposed price model and the real stock markets, which exhibits that the proposed model is feasible to some extent.

  4. An improved gray lattice Boltzmann model for simulating fluid flow in multi-scale porous media

    NASA Astrophysics Data System (ADS)

    Zhu, Jiujiang; Ma, Jingsheng

    2013-06-01

    A lattice Boltzmann (LB) model is proposed for simulating fluid flow in porous media by allowing the aggregates of finer-scale pores and solids to be treated as 'equivalent media'. This model employs a partially bouncing-back scheme to mimic the resistance of each aggregate, represented as a gray node in the model, to the fluid flow. Like several other lattice Boltzmann models that take the same approach, which are collectively referred to as gray lattice Boltzmann (GLB) models in this paper, it introduces an extra model parameter, ns, which represents a volume fraction of fluid particles to be bounced back by the solid phase rather than the volume fraction of the solid phase at each gray node. The proposed model is shown to conserve the mass even for heterogeneous media, while this model and that model of Walsh et al. (2009) [1], referred to the WBS model thereafter, are shown analytically to recover Darcy-Brinkman's equations for homogenous and isotropic porous media where the effective viscosity and the permeability are related to ns and the relaxation parameter of LB model. The key differences between these two models along with others are analyzed while their implications are highlighted. An attempt is made to rectify the misconception about the model parameter ns being the volume fraction of the solid phase. Both models are then numerically verified against the analytical solutions for a set of homogenous porous models and compared each other for another two sets of heterogeneous porous models of practical importance. It is shown that the proposed model allows true no-slip boundary conditions to be incorporated with a significant effect on reducing errors that would otherwise heavily skew flow fields near solid walls. The proposed model is shown to be numerically more stable than the WBS model at solid walls and interfaces between two porous media. The causes to the instability in the latter case are examined. The link between these two GLB models and a

  5. HPC Aspects of Variable-Resolution Global Climate Modeling using a Multi-scale Convection Parameterization

    EPA Science Inventory

    High performance computing (HPC) requirements for the new generation variable grid resolution (VGR) global climate models differ from that of traditional global models. A VGR global model with 15 km grids over the CONUS stretching to 60 km grids elsewhere will have about ~2.5 tim...

  6. Representative Structural Element - A New Paradigm for Multi-Scale Structural Modeling

    DTIC Science & Technology

    2016-07-05

    approach for efficient high-fidelity modeling of aerospace structures featuring multiscale heterogeneities and anisotropy. The proposed approach uses... efficiency ; representative structural element; micromechanics. 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF PAGES 469 19a...multiscale structural modeling to provide a systematic approach for efficient high-fidelity modeling of aerospace structures featuring multiscale

  7. The North American Carbon Program Multi-scale synthesis and Terrestrial Model Intercomparison Project Part 1: Overview and experimental design

    SciTech Connect

    Huntzinger, D.N.; Schwalm, C.; Michalak, A.M; Schaefer, K.; King, A.W.; Wei, Y.; Jacobson, A.; Liu, S.; Cook, R.; Post, W.M.; Berthier, G.; Hayes, D.; Huang, M.; Ito, A.; Lei, H.; Lu, C.; Mao, J.; Peng, C.H.; Peng, S.; Poulter, B.; Riccuito, D.; Shi, X.; Tian, H.; Wang, W.; Zeng, N.; Zhao, F.; Zhu, Q.

    2013-01-01

    Terrestrial biosphere models (TBMs) have become an integral tool for extrapolating local observations and understanding of land-atmosphere carbon exchange to larger regions. The North American Carbon Program (NACP) Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal model intercomparison and evaluation effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. MsTMIP builds upon current and past synthesis activities, and has a unique framework designed to isolate, interpret, and inform understanding of how model structural differences impact estimates of carbon uptake and release. Here we provide an overview of the MsTMIP effort and describe how the MsTMIP experimental design enables the assessment and quantification of TBM structural uncertainty. Model structure refers to the types of processes considered (e.g. nutrient cycling, disturbance, lateral transport of carbon), and how these processes are represented (e.g. photosynthetic formulation, temperature sensitivity, respiration) in the models. By prescribing a common experimental protocol with standard spin-up procedures and driver data sets, we isolate any biases and variability in TBM estimates of regional and global carbon budgets resulting from differences in the models themselves (i.e. model structure) and model-specific parameter values. An initial intercomparison of model structural differences is represented using hierarchical cluster diagrams (a.k.a. dendrograms), which highlight similarities and differences in how models account for carbon cycle, vegetation, energy, and nitrogen cycle dynamics. We show that, despite the standardized protocol used to derive initial conditions, models show a high degree of variation for GPP, total living biomass, and total soil carbon, underscoring the influence of differences in model structure and parameterization on model estimates.

  8. The North American Carbon Program Multi-scale synthesis and Terrestrial Model Intercomparison Project - Part 1: Overview and experimental design

    NASA Astrophysics Data System (ADS)

    Huntzinger, D. N.; Schwalm, C.; Michalak, A. M.; Schaefer, K.; King, A. W.; Wei, Y.; Jacobson, A.; Liu, S.; Cook, R. B.; Post, W. M.; Berthier, G.; Hayes, D.; Huang, M.; Ito, A.; Lei, H.; Lu, C.; Mao, J.; Peng, C. H.; Peng, S.; Poulter, B.; Riccuito, D.; Shi, X.; Tian, H.; Wang, W.; Zeng, N.; Zhao, F.; Zhu, Q.

    2013-07-01

    Terrestrial biosphere models (TBMs) have become an integral tool for extrapolating local observations and understanding of land-atmosphere carbon exchange to larger regions. The North American Carbon Program (NACP) Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal model intercomparison and evaluation effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. MsTMIP builds upon current and past synthesis activities, and has a unique framework designed to isolate, interpret, and inform understanding of how model structural differences impact estimates of carbon uptake and release. Here we provide an overview of the MsTMIP effort and describe how the MsTMIP experimental design enables the assessment and quantification of TBM structural uncertainty. Model structure refers to the types of processes considered (e.g. nutrient cycling, disturbance, lateral transport of carbon), and how these processes are represented (e.g. photosynthetic formulation, temperature sensitivity, respiration) in the models. By prescribing a common experimental protocol with standard spin-up procedures and driver data sets, we isolate any biases and variability in TBM estimates of regional and global carbon budgets resulting from differences in the models themselves (i.e. model structure) and model-specific parameter values. An initial intercomparison of model structural differences is represented using hierarchical cluster diagrams (a.k.a. dendrograms), which highlight similarities and differences in how models account for carbon cycle, vegetation, energy, and nitrogen cycle dynamics. We show that, despite the standardized protocol used to derive initial conditions, models show a high degree of variation for GPP, total living biomass, and total soil carbon, underscoring the influence of differences in model structure and parameterization on model estimates.

  9. The North American Carbon Program Multi-Scale Synthesis and Terrestrial Model Intercomparison Project - Part 1: Overview and experimental design

    NASA Astrophysics Data System (ADS)

    Huntzinger, D. N.; Schwalm, C.; Michalak, A. M.; Schaefer, K.; King, A. W.; Wei, Y.; Jacobson, A.; Liu, S.; Cook, R. B.; Post, W. M.; Berthier, G.; Hayes, D.; Huang, M.; Ito, A.; Lei, H.; Lu, C.; Mao, J.; Peng, C. H.; Peng, S.; Poulter, B.; Riccuito, D.; Shi, X.; Tian, H.; Wang, W.; Zeng, N.; Zhao, F.; Zhu, Q.

    2013-12-01

    Terrestrial biosphere models (TBMs) have become an integral tool for extrapolating local observations and understanding of land-atmosphere carbon exchange to larger regions. The North American Carbon Program (NACP) Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal model intercomparison and evaluation effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. MsTMIP builds upon current and past synthesis activities, and has a unique framework designed to isolate, interpret, and inform understanding of how model structural differences impact estimates of carbon uptake and release. Here we provide an overview of the MsTMIP effort and describe how the MsTMIP experimental design enables the assessment and quantification of TBM structural uncertainty. Model structure refers to the types of processes considered (e.g., nutrient cycling, disturbance, lateral transport of carbon), and how these processes are represented (e.g., photosynthetic formulation, temperature sensitivity, respiration) in the models. By prescribing a common experimental protocol with standard spin-up procedures and driver data sets, we isolate any biases and variability in TBM estimates of regional and global carbon budgets resulting from differences in the models themselves (i.e., model structure) and model-specific parameter values. An initial intercomparison of model structural differences is represented using hierarchical cluster diagrams (a.k.a. dendrograms), which highlight similarities and differences in how models account for carbon cycle, vegetation, energy, and nitrogen cycle dynamics. We show that, despite the standardized protocol used to derive initial conditions, models show a high degree of variation for GPP, total living biomass, and total soil carbon, underscoring the influence of differences in model structure and parameterization on model estimates.

  10. SAPHIR - a multi-scale, multi-resolution modeling environment targeting blood pressure regulation and fluid homeostasis.

    PubMed

    Thomas, S; Abdulhay, Enas; Baconnier, Pierre; Fontecave, Julie; Francoise, Jean-Pierre; Guillaud, Francois; Hannaert, Patrick; Hernandez, Alfredo; Le Rolle, Virginie; Maziere, Pierre; Tahi, Fariza; Zehraoui, Farida

    2007-01-01

    We present progress on a comprehensive, modular, interactive modeling environment centered on overall regulation of blood pressure and body fluid homeostasis. We call the project SAPHIR, for "a Systems Approach for PHysiological Integration of Renal, cardiac, and respiratory functions". The project uses state-of-the-art multi-scale simulation methods. The basic core model will give succinct input-output (reduced-dimension) descriptions of all relevant organ systems and regulatory processes, and it will be modular, multi-resolution, and extensible, in the sense that detailed submodules of any process(es) can be "plugged-in" to the basic model in order to explore, eg. system-level implications of local perturbations. The goal is to keep the basic core model compact enough to insure fast execution time (in view of eventual use in the clinic) and yet to allow elaborate detailed modules of target tissues or organs in order to focus on the problem area while maintaining the system-level regulatory compensations.

  11. Multi-scale problem in the model of RNA virus evolution

    NASA Astrophysics Data System (ADS)

    Korobeinikov, Andrei; Archibasov, Aleksei; Sobolev, Vladimir

    2016-06-01

    A mathematical or computational model in evolutionary biology should necessary combine several comparatively fast processes, which actually drive natural selection and evolution, with a very slow process of evolution. As a result, several very different time scales are simultaneously present in the model; this makes its analytical study an extremely difficult task. However, the significant difference of the time scales implies the existence of a possibility of the model order reduction through a process of time separation. In this paper we conduct the procedure of model order reduction for a reasonably simple model of RNA virus evolution reducing the original system of three integro-partial derivative equations to a single equation. Computations confirm that there is a good fit between the results for the original and reduced models.

  12. Multi-scale inference of interaction rules in animal groups using Bayesian model selection.

    PubMed

    Mann, Richard P; Perna, Andrea; Strömbom, Daniel; Garnett, Roman; Herbert-Read, James E; Sumpter, David J T; Ward, Ashley J W

    2012-01-01

    Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour. Models are tuned through repeated simulation until they match the observed behaviour. More recent work has used the fine scale motions of animals to validate and fit the rules of interaction of animals in groups. Here, we use a Bayesian methodology to compare a variety of models to the collective motion of glass prawns (Paratya australiensis). We show that these exhibit a stereotypical 'phase transition', whereby an increase in density leads to the onset of collective motion in one direction. We fit models to this data, which range from: a mean-field model where all prawns interact globally; to a spatial Markovian model where prawns are self-propelled particles influenced only by the current positions and directions of their neighbours; up to non-Markovian models where prawns have 'memory' of previous interactions, integrating their experiences over time when deciding to change behaviour. We show that the mean-field model fits the large scale behaviour of the system, but does not capture fine scale rules of interaction, which are primarily mediated by physical contact. Conversely, the Markovian self-propelled particle model captures the fine scale rules of interaction but fails to reproduce global dynamics. The most sophisticated model, the non-Markovian model, provides a good match to the data at both the fine scale and in terms of reproducing global dynamics. We conclude that prawns' movements are influenced by not just the current direction of nearby conspecifics, but also those encountered in the recent past. Given the simplicity of prawns as a study system our research suggests that self-propelled particle models of collective motion should, if they are to be realistic at multiple biological scales, include memory of previous interactions and other non-Markovian effects.

  13. Multi-scale inference of interaction rules in animal groups using Bayesian model selection.

    PubMed

    Mann, Richard P; Perna, Andrea; Strömbom, Daniel; Garnett, Roman; Herbert-Read, James E; Sumpter, David J T; Ward, Ashley J W

    2013-01-01

    Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour. Models are tuned through repeated simulation until they match the observed behaviour. More recent work has used the fine scale motions of animals to validate and fit the rules of interaction of animals in groups. Here, we use a Bayesian methodology to compare a variety of models to the collective motion of glass prawns (Paratya australiensis). We show that these exhibit a stereotypical 'phase transition', whereby an increase in density leads to the onset of collective motion in one direction. We fit models to this data, which range from: a mean-field model where all prawns interact globally; to a spatial Markovian model where prawns are self-propelled particles influenced only by the current positions and directions of their neighbours; up to non-Markovian models where prawns have 'memory' of previous interactions, integrating their experiences over time when deciding to change behaviour. We show that the mean-field model fits the large scale behaviour of the system, but does not capture the observed locality of interactions. Traditional self-propelled particle models fail to capture the fine scale dynamics of the system. The most sophisticated model, the non-Markovian model, provides a good match to the data at both the fine scale and in terms of reproducing global dynamics, while maintaining a biologically plausible perceptual range. We conclude that prawns' movements are influenced by not just the current direction of nearby conspecifics, but also those encountered in the recent past. Given the simplicity of prawns as a study system our research suggests that self-propelled particle models of collective motion should, if they are to be realistic at multiple biological scales, include memory of previous interactions and other non-Markovian effects.

  14. Evaluation of the Community Multi-scale Air Quality Model Version 5.2

    EPA Science Inventory

    The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...

  15. Evaluation of the Community Multi-scale Air Quality (CMAQ) Model Version 5.2

    EPA Science Inventory

    The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...

  16. Evaluation of the Community Multi-scale Air Quality (CMAQ) Model Version 5.1

    EPA Science Inventory

    The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...

  17. Towards a virtual lung: multi-scale, multi-physics modelling of the pulmonary system

    PubMed Central

    Burrowes, K.S; Swan, A.J; Warren, N.J; Tawhai, M.H

    2008-01-01

    The essential function of the lung, gas exchange, is dependent on adequate matching of ventilation and perfusion, where air and blood are delivered through complex branching systems exposed to regionally varying transpulmonary and transmural pressures. Structure and function in the lung are intimately related, yet computational models in pulmonary physiology usually simplify or neglect structure. The geometries of the airway and vascular systems and their interaction with parenchymal tissue have an important bearing on regional distributions of air and blood, and therefore on whole lung gas exchange, but this has not yet been addressed by modelling studies. Models for gas exchange have typically incorporated considerable detail at the level of chemical reactions, with little thought for the influence of structure. To date, relatively little attention has been paid to modelling at the cellular or subcellular level in the lung, or to linking information from the protein structure/interaction and cellular levels to the operation of the whole lung. We review previous work in developing anatomically based models of the lung, airways, parenchyma and pulmonary vasculature, and some functional studies in which these models have been used. Models for gas exchange at several spatial scales are briefly reviewed, and the challenges and benefits from modelling cellular function in the lung are discussed. PMID:18593661

  18. Adaptive Remodeling of Achilles Tendon: A Multi-scale Computational Model

    PubMed Central

    Rubenson, Jonas; Umberger, Brian

    2016-01-01

    While it is known that musculotendon units adapt to their load environments, there is only a limited understanding of tendon adaptation in vivo. Here we develop a computational model of tendon remodeling based on the premise that mechanical damage and tenocyte-mediated tendon damage and repair processes modify the distribution of its collagen fiber lengths. We explain how these processes enable the tendon to geometrically adapt to its load conditions. Based on known biological processes, mechanical and strain-dependent proteolytic fiber damage are incorporated into our tendon model. Using a stochastic model of fiber repair, it is assumed that mechanically damaged fibers are repaired longer, whereas proteolytically damaged fibers are repaired shorter, relative to their pre-damage length. To study adaptation of tendon properties to applied load, our model musculotendon unit is a simplified three-component Hill-type model of the human Achilles-soleus unit. Our model results demonstrate that the geometric equilibrium state of the Achilles tendon can coincide with minimization of the total metabolic cost of muscle activation. The proposed tendon model independently predicts rates of collagen fiber turnover that are in general agreement with in vivo experimental measurements. While the computational model here only represents a first step in a new approach to understanding the complex process of tendon remodeling in vivo, given these findings, it appears likely that the proposed framework may itself provide a useful theoretical foundation for developing valuable qualitative and quantitative insights into tendon physiology and pathology. PMID:27684554

  19. The Radiative Properties of Small Clouds: Multi-Scale Observations and Modeling

    SciTech Connect

    Feingold, Graham; McComiskey, Allison

    2013-09-25

    Warm, liquid clouds and their representation in climate models continue to represent one of the most significant unknowns in climate sensitivity and climate change. Our project combines ARM observations, LES modeling, and satellite imagery to characterize shallow clouds and the role of aerosol in modifying their radiative effects.

  20. Multi-scale modeling for the self-assembly of DNA-functionalized nanoparticle into supperlattice and Wulff polydedra

    NASA Astrophysics Data System (ADS)

    Li, Ting; Auyeung, Evelyn; Mirkin, Chad; Olvera de La Cruz, Monica; Northwestern University Team

    2014-03-01

    Since 1996, DNA hybridization has proven robust for programmable self-assembly of nanoparticles (NPs). Recently, we showed that through a ``slow cooling'' method, DNA functionalized nanospheres or so-called ``programmable atom equivalents'' can assemble into crystals with a specific and uniform habit. Here we perform molecular dynamics simulations on multi-scale models to study and predict the corresponding shapes. Firstly, we use a scale-accurate coarse-grained model with explicit DNA chains to estimate surface energy ratios for different surface orientations, and predict the corresponding Wulff polyhedra based on these values. Secondly, we use a colloidal model in which each DNA coated nanosphere is represented by a single bead to simulate the growth dynamics of the crystals. By this method, we confirm the shape for the body-centered-cubic system to be a (110)-enclosed rhombic dodecahedron. But the face-centered-cubic system does not show any uniform shape yet except triangular features with (111) and (100) facets due to crystallographic defects including twinning and stacking faults. These simulated crystal shapes agrees very well with experiments. Air Force Office of Scientific Research (AFOSR) Multidisciplinary University Research Initiative (MURI) FA9550-11-1-0275.

  1. A Robust Multi-Scale Modeling System for the Study of Cloud and Precipitation Processes

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2012-01-01

    During the past decade, numerical weather and global non-hydrostatic models have started using more complex microphysical schemes originally developed for high resolution cloud resolving models (CRMs) with 1-2 km or less horizontal resolutions. These microphysical schemes affect the dynamic through the release of latent heat (buoyancy loading and pressure gradient) the radiation through the cloud coverage (vertical distribution of cloud species), and surface processes through rainfall (both amount and intensity). Recently, several major improvements of ice microphysical processes (or schemes) have been developed for cloud-resolving model (Goddard Cumulus Ensemble, GCE, model) and regional scale (Weather Research and Forecast, WRF) model. These improvements include an improved 3-ICE (cloud ice, snow and graupel) scheme (Lang et al. 2010); a 4-ICE (cloud ice, snow, graupel and hail) scheme and a spectral bin microphysics scheme and two different two-moment microphysics schemes. The performance of these schemes has been evaluated by using observational data from TRMM and other major field campaigns. In this talk, we will present the high-resolution (1 km) GeE and WRF model simulations and compared the simulated model results with observation from recent field campaigns [i.e., midlatitude continental spring season (MC3E; 2010), high latitude cold-season (C3VP, 2007; GCPEx, 2012), and tropical oceanic (TWP-ICE, 2006)].

  2. Microphysics in Multi-scale Modeling System with Unified Physics (Invited)

    NASA Astrophysics Data System (ADS)

    Tao, W.; Lang, S. E.; Wu, D.; Chern, J.

    2013-12-01

    Recently, several major improvements of ice microphysical processes (or schemes) have been developed for cloud-resolving models (Goddard Cumulus Ensemble, GCE, model), regional scale (Weather Research and Forecast, WRF) model and MMF. These improvements include an improved 3-ICE (cloud ice, snow and graupel) scheme (Lang et al. 2011); a 4-ICE (cloud ice, snow, graupel and hail; Lang et al. 2013) scheme and a spectral bin microphysics scheme and two different two-moment microphysics schemes. These models have improved the radiative processes and their interactions with cloud and aerosol. The performance of these schemes has been evaluated by using observational data from TRMM and major field campaigns. In this talk, we will present high-resolution GCE, WRF and MMF model simulations and compare the model results with observations [i.e., Typhoon (Morakot 2009 - an updated simulations), Anvil and Aerosol (AMMA 2006); MCSs (MC3E; 2010; diurnal variation) and CloudSat/TRMM]. In addition, the main issues of the microphysics schemes in high-resolution (1-6 km grid spacing) numerical models will be discussed.

  3. Determinants of wood thrush nest success: A multi-scale, model selection approach

    USGS Publications Warehouse

    Driscoll, M.J.L.; Donovan, T.; Mickey, R.; Howard, A.; Fleming, K.K.

    2005-01-01

    We collected data on 212 wood thrush (Hylocichla mustelina) nests in central New York from 1998 to 2000 to determine the factors that most strongly influence nest success. We used an information-theoretic approach to assess and rank 9 models that examined the relationship between nest success (i.e., the probability that a nest would successfully fledge at least 1 wood thrush offspring) and habitat conditions at different spatial scales. We found that 4 variables were significant predictors of nesting success for wood thrushes: (1) total core habitat within 5 km of a study site, (2) distance to forest-field edge, (3) total forest cover within 5 km of the study site, and (4) density and variation in diameter of trees and shrubs surrounding the nest. The coefficients of these predictors were all positive. Of the 9 models evaluated, amount of core habitat in the 5-km landscape was the best-fit model, but the vegetation structure model (i.e., the density of trees and stems surrounding a nest) was also supported by the data. Based on AIC weights, enhancement of core area is likely to be a more effective management option than any other habitat-management options explored in this study. Bootstrap analysis generally confirmed these results; core and vegetation structure models were ranked 1, 2, or 3 in over 50% of 1,000 bootstrap trials. However, bootstrap results did not point to a decisive model, which suggests that multiple habitat factors are influencing wood thrush nesting success. Due to model uncertainty, we used a model averaging approach to predict the success or failure of each nest in our dataset. This averaged model was able to correctly predict 61.1% of nest outcomes.

  4. Community Multi-scale Air Quality (CMAQ) Modeling System for Air Quality Management

    EPA Pesticide Factsheets

    CMAQ simultaneously models multiple air pollutants including ozone, particulate matter and a variety of air toxics to help air quality managers determine the best air quality management scenarios for their communities, regions and states.

  5. The Sub-Arctic Carbon Cycle: Assimilating Multi-Scale Chamber, Tower and Aircraft Flux Observations into Ecological Models

    NASA Astrophysics Data System (ADS)

    Hill, T. C.; Stoy, P. C.; Baxter, R.; Clement, R.; Disney, M.; Evans, J.; Fletcher, B.; Gornall, J.; Harding, R.; Hartley, I. P.; Ineson, P.; Moncrieff, J.; Phoenix, G.; Sloan, V.; Poyatos, R.; Prieto-Blanco, A.; Subke, J.; Street, L.; Wade, T. J.; Wayolle, A.; Wookey, P.; Williams, M. D.

    2009-12-01

    source/sink status of the landscapes, but cold season data were successfully collected. Aircraft flux measurements during the peak growing season provided an estimate of landscape variability alongside the temporal sampling from fixed tower systems, and a means to constrain upscaling via models. Assimilation of these multi-scale data into an ecosystem carbon model yielded improved constraints on processes, particularly the turnover rates of soil carbon. Our work shows that these improvements cannot be attained with a single source of data (chamber, tower or aircraft).

  6. Multi-scaling in the Cont-Bouchaud microscopic stock market model

    NASA Astrophysics Data System (ADS)

    Castiglione, Filippo; Stauffer, Dietrich

    2001-11-01

    The Cont-Bouchaud percolation model is one of the simplest microsimulation models yet able to account for the main stylized fact of financial markets, e.g. fat tails of the histogram of log-returns. In the present paper we show that for a certain range of the parameters it is possible to generate price time-series that cannot be described in terms of a unique scaling exponent.

  7. Multi-scale evaluation of ISIMIP biome models against NDVI and MODIS NPP data

    NASA Astrophysics Data System (ADS)

    Rafique, Rashad; Zhao, Fang; Zeng, Ning; Asrar, Ghassem; Reyer, Christopher; Ostberg, Sebastian; Francois, Louis; Tian, Hanqin; Chnag, Jinfeng; Nishina, Kazuya

    2016-04-01

    The net primary productivity (NPP) is commonly used for understanding the dynamics of terrestrial ecosystems and their role in carbon cycle. The global NPP, highly variable over space and time, cannot be directly observed, therefore, satellite based observations of Normalized Difference Vegetation Index (NDVI) are used as a proxy to understand and monitor the NPP dynamics. In this study, we used a combination of most recent NDVI and modeled NPP data for the period 1982-2012, to study the role of terrestrial ecosystems in carbon cycle under the prevailing climate conditions. We found that in general there is good agreement between the spatial patterns and global seasonal cycles between observed NDVI and modeled NPP values. Simulated NPP values also generally agree with MODIS NPP spatially, and temporally, MODIS NPP falls within the model spread of NPP values. Despite of the general agreement in the trends of global total NDVI, MODIS NPP and modeled NPP, considerable spatial differences are found, and the ensemble mean of the models often agrees better with the spatial patterns of observed NDVI and MODIS NPP than individual models.

  8. Multi-scale hydrometeorological observation and modelling strategy for flash-flood understanding

    NASA Astrophysics Data System (ADS)

    Braud, Isabelle

    2014-05-01

    Flash floods are a major natural hazard, especially in the Mediterranean region, but their predictability remains low due to high non-linearity in the hydrological response related to threshold effects and structured-heterogeneity at all scales. In this paper, we propose a coupled observation and modelling strategy aiming at improving the understanding of processes triggering flash floods. This strategy is illustrated for the Mediterranean area using two French catchments (Gard and Ardèche) larger than 2000 km². The experimental approach is based on the monitoring of nested spatial scales: 1/ the hillslope scale, where processes influencing the runoff generation and its concentration can be tackled; 2/ the small to medium catchment scale (1-100 km²) where the impact of the network structure and of the spatial variability of rainfall, landscape and initial soil moisture can be quantified; 3/ the larger scale (100-1000 km²) where the river routing and flooding processes become important. These observations are part of the HyMeX (Hydrological Cycle in the Mediterranean Experiment) Enhanced Observation Period (EOP) and lasts four years (2012-2015). In terms of hydrological modelling the objective is to set up models at the regional scale, while addressing small and generally ungauged catchments, which is the scale of interest for flooding risk assessment. Top-down and bottom-up approaches are combined and the models are used as "hypothesis testing" tools by coupling model development with data analyses, in order to incrementally evaluate the validity of model hypotheses. The paper focuses on the presentation of the experimental strategy and the instrumentation, with first results obtained during the first years of the experiment. The perspectives in terms of modelling are also presented.

  9. Multi-scale modeling of multi-component reactive transport in geothermal aquifers

    NASA Astrophysics Data System (ADS)

    Nick, Hamidreza M.; Raoof, Amir; Wolf, Karl-Heinz; Bruhn, David

    2014-05-01

    In deep geothermal systems heat and chemical stresses can cause physical alterations, which may have a significant effect on flow and reaction rates. As a consequence it will lead to changes in permeability and porosity of the formations due to mineral precipitation and dissolution. Large-scale modeling of reactive transport in such systems is still challenging. A large area of uncertainty is the way in which the pore-scale information controlling the flow and reaction will behave at a larger scale. A possible choice is to use constitutive relationships relating, for example the permeability and porosity evolutions to the change in the pore geometry. While determining such relationships through laboratory experiments may be limited, pore-network modeling provides an alternative solution. In this work, we introduce a new workflow in which a hybrid Finite-Element Finite-Volume method [1,2] and a pore network modeling approach [3] are employed. Using the pore-scale model, relevant constitutive relations are developed. These relations are then embedded in the continuum-scale model. This approach enables us to study non-isothermal reactive transport in porous media while accounting for micro-scale features under realistic conditions. The performance and applicability of the proposed model is explored for different flow and reaction regimes. References: 1. Matthäi, S.K., et al.: Simulation of solute transport through fractured rock: a higher-order accurate finite-element finite-volume method permitting large time steps. Transport in porous media 83.2 (2010): 289-318. 2. Nick, H.M., et al.: Reactive dispersive contaminant transport in coastal aquifers: Numerical simulation of a reactive Henry problem. Journal of contaminant hydrology 145 (2012), 90-104. 3. Raoof A., et al.: PoreFlow: A Complex pore-network model for simulation of reactive transport in variably saturated porous media, Computers & Geosciences, 61, (2013), 160-174.

  10. Design strategies for human & earth systems modeling to meet emerging multi-scale decision support needs

    NASA Astrophysics Data System (ADS)

    Spak, S.; Pooley, M.

    2012-12-01

    The next generation of coupled human and earth systems models promises immense potential and grand challenges as they transition toward new roles as core tools for defining and living within planetary boundaries. New frontiers in community model development include not only computational, organizational, and geophysical process questions, but also the twin objectives of more meaningfully integrating the human dimension and extending applicability to informing policy decisions on a range of new and interconnected issues. We approach these challenges by posing key policy questions that require more comprehensive coupled human and geophysical models, identify necessary model and organizational processes and outputs, and work backwards to determine design criteria in response to these needs. We find that modular community earth system model design must: * seamlessly scale in space (global to urban) and time (nowcasting to paleo-studies) and fully coupled on all component systems * automatically differentiate to provide complete coupled forward and adjoint models for sensitivity studies, optimization applications, and 4DVAR assimilation across Earth and human observing systems * incorporate diagnostic tools to quantify uncertainty in couplings, and in how human activity affects them * integrate accessible community development and application with JIT-compilation, cloud computing, game-oriented interfaces, and crowd-sourced problem-solving We outline accessible near-term objectives toward these goals, and describe attempts to incorporate these design objectives in recent pilot activities using atmosphere-land-ocean-biosphere-human models (WRF-Chem, IBIS, UrbanSim) at urban and regional scales for policy applications in climate, energy, and air quality.

  11. Theory and simulations of a multi-scale magnetotail current sheet model

    NASA Astrophysics Data System (ADS)

    Sitnov, M. I.; Swisdak, M. M.; Guzdar, P. N.

    2010-12-01

    One of the key problems in modeling of the solar wind-magnetosphere interaction is the description of the magnetotail reconnection onset. It is widely accepted, that the explosive release of energy accumulated in the magnetotail, which occurs during substorms and bursty bulk flows, must involve some form of unsteady magnetic reconnection. However, the specific features of the magnetotail reconnection and its proper description at the kinetic level, not to speak about its reduced form suitable for global MHD modeling, remain poorly understood. Moreover, until recently the onset of spontaneous reconnection was thought to be fully prohibited, because the sufficient stability criterion of the corresponding plasma wave, the ion tearing mode, was fulfilled within the WKB approximation for all types of the considered magnetotail equilibria. Recently it was found (Sitnov and Schindler, 2010), that the ion tearing stability criterion might be relaxed in the tail current sheet models, which have more than two characteristic spatial scales. In particular, the substantial tearing destabilization takes place for equilibria with accumulation of the magnetic flux at the tailward end of an extended thin current sheet. We consider generalizations of the Sitnov-Schindler model including seed X-lines, and analyze their linear and nonlinear stability properties, as well as implications of the new stability criterion for global MHD models. The nonlinear stability issues are investigated with the help of an open-boundary modification of the full-particle code P3D (Zeiler et al., 2002).

  12. A Multi-Scale Computational Model for the Study of Retinal Prosthetic Stimulation

    PubMed Central

    Loizos, Kyle; Lazzi, Gianluca; Lauritzen, J. Scott; Anderson, James; Jones, Bryan W.; Marc, Robert

    2015-01-01

    An implantable retinal prosthesis has been developed to restore vision to patients who have been blinded by degenerative diseases that destroy photoreceptors. By electrically stimulating the surviving retinal cells, the damaged photoreceptors may be bypassed and limited vision can be restored. While this has been shown to restore partial vision, the understanding of how cells react to this systematic electrical stimulation is largely unknown. Better predictive models and a deeper understanding of neural responses to electrical stimulation is necessary for designing a successful prosthesis. In this work, a computational model of an epi-retinal implant was built and simulated, spanning multiple spatial scales, including a large-scale model of the retina and implant electronics, as well as underlying neuronal networks. PMID:25571389

  13. Capturing recrystallization of metals with a multi-scale materials model

    SciTech Connect

    D. A. Hughes; D. J. Bammann; A. Godfrey; V. C. Prantil; E. A. Holm; M. A. Miodownik; D. C. Chrzan; M. T. Lusk

    2000-04-01

    The final report for a Laboratory Directed Research and Development project entitled, ``Capturing Recrystallization of Metals in a Multiscale Materials Model'' is presented. In this project, deformation and recrystallization processes have been followed experimentally and theoretically in order to incorporate essential mechanisms from the defect (dislocation) and grain size length scales. A nonlinear rotational gradient theory has been developed which enables the incorporation of microstructural parameters. The evolution of these parameters during deformation and recrystallization has been characterized qualitatively and quantitatively, applying various electron optic techniques ranging over several length scales. The theoretical and experimental framework developed is general. It has been exemplified by an application to recrystallization in single crystals and bicrystals of aluminum. The recrystallization process has been modeled using a 3-D model for the changes in key structural parameters during recrystallization.

  14. Effects of Energy Development on Hydrologic Response: a Multi-Scale Modeling Approach

    NASA Astrophysics Data System (ADS)

    Vithanage, J.; Miller, S. N.; Berendsen, M.; Caffrey, P. A.; Bellis, J.; Schuler, R.

    2013-12-01

    Potential impacts of energy development on surface hydrology in western Wyoming were assessed using spatially explicit hydrological models. Currently there are proposals to develop over 800 new oil and gas wells in the 218,000 acre-sized LaBarge development area that abuts the Wyoming Range and contributes runoff to the Upper Green River (approximately 1 well per 2 square miles). The intensity of development raises questions relating to impacts on the hydrological cycle, water quality, erosion and sedimentation. We developed landscape management scenarios relating to current disturbance and proposed actions put forth by the energy operators to provide inputs to spatially explicit hydrologic models. Differences between the scenarios were derived to quantify the changes and analyse the impacts to the project area. To perform this research, the Automated Watershed Assessment Tool (AGWA) was enhanced by adding different management practices suitable for the region, including the reclamation of disturbed lands over time. The AGWA interface was used to parameterize and execute two hydrologic models: the Soil and Water Assessment Tool (SWAT) and the KINEmatic Runoff and EROSion model (KINEROS2). We used freely available data including SSURGO soils, Multi-Resolution Landscape Consortium (MRLC) land cover, and 10m resolution terrain data to derive suitable initial parameters for the models. The SWAT model was manually calibrated using an innovative method at the monthly level; observed daily rainfall and temperature inputs were used as a function of elevation considering the local climate effects. Higher temporal calibration was not possible due to a lack of adequate climate and runoff data. The Nash Sutcliff efficiencies of two calibrated watersheds at the monthly scale exceeded 0.95. Results of the AGWA/SWAT simulations indicate a range of sensitivity to disturbance due to heterogeneous soil and terrain characteristics over a simulated time period of 10 years. The KINEROS

  15. Multi-scale computational model of three-dimensional hemodynamics within a deformable full-body arterial network

    SciTech Connect

    Xiao, Nan; Humphrey, Jay D.; Figueroa, C. Alberto

    2013-07-01

    In this article, we present a computational multi-scale model of fully three-dimensional and unsteady hemodynamics within the primary large arteries in the human. Computed tomography image data from two different patients were used to reconstruct a nearly complete network of the major arteries from head to foot. A linearized coupled-momentum method for fluid–structure-interaction was used to describe vessel wall deformability and a multi-domain method for outflow boundary condition specification was used to account for the distal circulation. We demonstrated that physiologically realistic results can be obtained from the model by comparing simulated quantities such as regional blood flow, pressure and flow waveforms, and pulse wave velocities to known values in the literature. We also simulated the impact of age-related arterial stiffening on wave propagation phenomena by progressively increasing the stiffness of the central arteries and found that the predicted effects on pressure amplification and pulse wave velocity are in agreement with findings in the clinical literature. This work demonstrates the feasibility of three-dimensional techniques for simulating hemodynamics in a full-body compliant arterial network.

  16. On multi-scale percolation behaviour of the effective conductivity for the lattice model with interacting particles

    NASA Astrophysics Data System (ADS)

    Wiśniowski, R.; Olchawa, W.; Frączek, D.; Piasecki, R.

    2016-02-01

    Recently, the effective medium approach (EMA) using 2×2 basic cluster of model lattice sites to predict the conductivity of interacting microemulsion droplets has been presented by Hattori et al. To make a step aside from pure applications, we studied earlier a multi-scale percolation, employing any k× k basic cluster for non-interacting particles. Here, with interactions included, we examine in what way they alter the percolation threshold for any cluster case. We found that at a fixed length scale k, the interaction reduces the range of shifts of the percolation threshold. To determine the critical concentrations, the simplified EMA-model is used. It diminishes the number of local conductivities into two main ones. In the presence of a dominance of the repulsive interaction over the thermal energy, the exact percolation thresholds at two small scales can be revealed from analytical formulas. Furthermore, at large scales, the highest possible value of the estimated threshold can be obtained.

  17. Exploiting multi-scale parallelism for large scale numerical modelling of laser wakefield accelerators

    NASA Astrophysics Data System (ADS)

    Fonseca, R. A.; Vieira, J.; Fiuza, F.; Davidson, A.; Tsung, F. S.; Mori, W. B.; Silva, L. O.

    2013-12-01

    A new generation of laser wakefield accelerators (LWFA), supported by the extreme accelerating fields generated in the interaction of PW-Class lasers and underdense targets, promises the production of high quality electron beams in short distances for multiple applications. Achieving this goal will rely heavily on numerical modelling to further understand the underlying physics and identify optimal regimes, but large scale modelling of these scenarios is computationally heavy and requires the efficient use of state-of-the-art petascale supercomputing systems. We discuss the main difficulties involved in running these simulations and the new developments implemented in the OSIRIS framework to address these issues, ranging from multi-dimensional dynamic load balancing and hybrid distributed/shared memory parallelism to the vectorization of the PIC algorithm. We present the results of the OASCR Joule Metric program on the issue of large scale modelling of LWFA, demonstrating speedups of over 1 order of magnitude on the same hardware. Finally, scalability to over ˜106 cores and sustained performance over ˜2 P Flops is demonstrated, opening the way for large scale modelling of LWFA scenarios.

  18. Reversability of arctic sea ice retreat - A conceptual multi-scale modeling approach

    NASA Astrophysics Data System (ADS)

    Mueller-Stoffels, Marc

    The ice-albedo feedback has been identified as an important factor in the decay of the Arctic sea ice cover in a warming climate. Mechanisms of transition from perennial ice cover to seasonal ice cover are discussed in the literature; the existence of a tipping point is disputed. A newly developed regular network model for energy exchange and phase transition of an ice covered ocean mixed layer is introduced. The existence of bistability, a key ingredient for irreversibility, on local and regional scales is explored. It is shown in a spatially confined model that the asymptotic behavior and the existence of a parameter region of bistability strongly depend on the albedo parametrization. The spatial dynamics of sea ice retreat are studied for a high resolution latitudinal model of the ocean mixed layer. This regional model suggests that sea ice retreat is reversible. It is shown that laterally driven melt of thick multi-year sea ice, and thus, ice-albedo feedback, is an important mechanism in the transition from perennial to seasonal ice cover at the pole. Results are used to interpret observed changes in the recent ice extent and ice volume record. It is shown that the effectiveness of ice-albedo feedback strongly depends on the existence of lateral heat transfer mechanisms in the ocean.

  19. Evaluation of Cartosat-1 Multi-Scale Digital Surface Modelling Over France

    PubMed Central

    Gianinetto, Marco

    2009-01-01

    On 5 May 2005, the Indian Space Research Organization launched Cartosat-1, the eleventh satellite of its constellation, dedicated to the stereo viewing of the Earth's surface for terrain modeling and large-scale mapping, from the Satish Dhawan Space Centre (India). In early 2006, the Indian Space Research Organization started the Cartosat-1 Scientific Assessment Programme, jointly established with the International Society for Photogrammetry and Remote Sensing. Within this framework, this study evaluated the capabilities of digital surface modeling from Cartosat-1 stereo data for the French test sites of Mausanne les Alpilles and Salon de Provence. The investigation pointed out that for hilly territories it is possible to produce high-resolution digital surface models with a root mean square error less than 7.1 m and a linear error at 90% confidence level less than 9.5 m. The accuracy of the generated digital surface models also fulfilled the requirements of the French Reference 3D®, so Cartosat-1 data may be used to produce or update such kinds of products. PMID:22412311

  20. Northeast Coastal Ocean Forecast System (NECOFS): A Multi-scale Global-Regional-Estuarine FVCOM Model

    NASA Astrophysics Data System (ADS)

    Beardsley, R. C.; Chen, C.

    2014-12-01

    The Northeast Coastal Ocean Forecast System (NECOFS) is a global-regional-estuarine integrated atmosphere/surface wave/ocean forecast model system designed for the northeast US coastal region covering a computational domain from central New Jersey to the eastern end of the Scotian Shelf. The present system includes 1) the mesoscale meteorological model WRF (Weather Research and Forecasting); 2) the regional-domain FVCOM covering the Gulf of Maine/Georges Bank/New England Shelf region (GOM-FVCOM); 3) the unstructured-grid surface wave model (FVCOM-SWAVE) modified from SWAN with the same domain as GOM-FVCOM; 3) the Mass coastal FVCOM with inclusion of inlets, estuaries and intertidal wetlands; and 4) three subdomain wave-current coupled inundation FVCOM systems in Scituate, MA, Hampton River, NH and Mass Bay, MA. GOM-FVCOM grid features unstructured triangular meshes with horizontal resolution of ~ 0.3-25 km and a hybrid terrain-following vertical coordinate with a total of 45 layers. The Mass coastal FVCOM grid is configured with triangular meshes with horizontal resolution up to ~10 m, and 10 layers in the vertical. Scituate, Hampton River and Mass Bay inundation model grids include both water and land with horizontal resolution up to ~5-10 m and 10 vertical layers. GOM-FVCOM is driven by surface forcing from WRF model output configured for the region (with 9-km resolution), the COARE3 bulk air-sea flux algorithm, local river discharges, and tidal forcing constructed by eight constituents and subtidal forcing on the boundary nested to the Global-FVCOM. SWAVE is driven by the same WRF wind field with wave forcing at the boundary nested to Wave Watch III configured for the northwestern Atlantic region. The Mass coastal FVCOM and three inundation models are connected with GOM-FVCOM through one-way nesting in the common boundary zones. The Mass coastal FVCOM is driven by the same surface forcing as GOM-FVCOM. The nesting boundary conditions for the inundation models

  1. Multi-scale Hydrologic Modeling of the White Sands Dune Field, New Mexico

    NASA Astrophysics Data System (ADS)

    Bourret, S. M.; Newton, B. T.

    2014-12-01

    The shallow groundwater flow system of White Sands dune field, located within the arid to semi-arid Tularosa Basin of Southern New Mexico, likely stabilizes the base of the largest gypsum dune field in the world. The dune is saturated throughout nearly its entire accumulation thickness, resulting in a shallow water table (< 3 ft bgs) in the inter-dunal areas. Water table elevation influences the spatial extent of the dune field and accumulation thickness. The White Sands National Monument (WHSA) is concerned that lowering the water table may lead to increased scour and migration of the dune field, which could be unfavorable to the preservation of the flora and fauna that have adapted to survive there. In response to projected increases in groundwater pumping in the regional Tularosa Basin groundwater system, changes in surface water use, and the threat of climate change, the WHSA is interested in understanding how these changes on a regional scale may impact the shallow dune field aquifer. Mathematical modeling techniques on varying spatial and temporal scales are used to characterize the relative importance of the sources of water (local vs. regional) to the dune aquifer, and to quantify the timescales on which changes may affect the water table in the dune field. A 2-dimensional, dune-scale heat and fluid flow model uses the seasonal temperature fluctuations to estimate the vertical and horizontal flow of water from the regional system to the dune field aquifer. We have also constructed a 2-dimensional, hydrologic model to characterize the regional groundwater flow regime near to the dune aquifer system, as well as across the Tularosa Basin to a depth of 6 km. Additionally, a 3-dimensional, hydrologic model of the Tularosa Basin and the White Sands dune field quantifies hydrologic characteristics, sources and sinks of groundwater in the basin and at the dune field. Computed and observed salinity, groundwater residence times, and water level data are the primary

  2. A multi-scale comparison of modeled and observed seasonal methane emissions in northern wetlands

    NASA Astrophysics Data System (ADS)

    Xu, Xiyan; Riley, William J.; Koven, Charles D.; Billesbach, Dave P.; Chang, Rachel Y.-W.; Commane, Róisín; Euskirchen, Eugénie S.; Hartery, Sean; Harazono, Yoshinobu; Iwata, Hiroki; McDonald, Kyle C.; Miller, Charles E.; Oechel, Walter C.; Poulter, Benjamin; Raz-Yaseef, Naama; Sweeney, Colm; Torn, Margaret; Wofsy, Steven C.; Zhang, Zhen; Zona, Donatella

    2016-09-01

    Wetlands are the largest global natural methane (CH4) source, and emissions between 50 and 70° N latitude contribute 10-30 % to this source. Predictive capability of land models for northern wetland CH4 emissions is still low due to limited site measurements, strong spatial and temporal variability in emissions, and complex hydrological and biogeochemical dynamics. To explore this issue, we compare wetland CH4 emission predictions from the Community Land Model 4.5 (CLM4.5-BGC) with site- to regional-scale observations. A comparison of the CH4 fluxes with eddy flux data highlighted needed changes to the model's estimate of aerenchyma area, which we implemented and tested. The model modification substantially reduced biases in CH4 emissions when compared with CarbonTracker CH4 predictions. CLM4.5 CH4 emission predictions agree well with growing season (May-September) CarbonTracker Alaskan regional-level CH4 predictions and site-level observations. However, CLM4.5 underestimated CH4 emissions in the cold season (October-April). The monthly atmospheric CH4 mole fraction enhancements due to wetland emissions are also assessed using the Weather Research and Forecasting-Stochastic Time-Inverted Lagrangian Transport (WRF-STILT) model coupled with daily emissions from CLM4.5 and compared with aircraft CH4 mole fraction measurements from the Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) campaign. Both the tower and aircraft analyses confirm the underestimate of cold-season CH4 emissions by CLM4.5. The greatest uncertainties in predicting the seasonal CH4 cycle are from the wetland extent, cold-season CH4 production and CH4 transport processes. We recommend more cold-season experimental studies in high-latitude systems, which could improve the understanding and parameterization of ecosystem structure and function during this period. Predicted CH4 emissions remain uncertain, but we show here that benchmarking against observations across spatial scales can

  3. 3D Visualization of Hydrological Model Outputs For a Better Understanding of Multi-Scale Phenomena

    NASA Astrophysics Data System (ADS)

    Richard, J.; Schertzer, D. J. M.; Tchiguirinskaia, I.

    2014-12-01

    During the last decades, many hydrological models has been created to simulate extreme events or scenarios on catchments. The classical outputs of these models are 2D maps, time series or graphs, which are easily understood by scientists, but not so much by many stakeholders, e.g. mayors or local authorities, and the general public. One goal of the Blue Green Dream project is to create outputs that are adequate for them. To reach this goal, we decided to convert most of the model outputs into a unique 3D visualization interface that combines all of them. This conversion has to be performed with an hydrological thinking to keep the information consistent with the context and the raw outputs.We focus our work on the conversion of the outputs of the Multi-Hydro (MH) model, which is physically based, fully distributed and with a GIS data interface. MH splits the urban water cycle into 4 components: the rainfall, the surface runoff, the infiltration and the drainage. To each of them, corresponds a modeling module with specific inputs and outputs. The superimposition of all this information will highlight the model outputs and help to verify the quality of the raw input data. For example, the spatial and the time variability of the rain generated by the rainfall module will be directly visible in 4D (3D + time) before running a full simulation. It is the same with the runoff module: because the result quality depends of the resolution of the rasterized land use, it will confirm or not the choice of the cell size.As most of the inputs and outputs are GIS files, two main conversions will be applied to display the results into 3D. First, a conversion from vector files to 3D objects. For example, buildings are defined in 2D inside a GIS vector file. Each polygon can be extruded with an height to create volumes. The principle is the same for the roads but an intrusion, instead of an extrusion, is done inside the topography file. The second main conversion is the raster

  4. Hierarchical analysis and multi-scale modelling of rat cortical and trabecular bone

    PubMed Central

    Oftadeh, Ramin; Entezari, Vahid; Spörri, Guy; Villa-Camacho, Juan C.; Krigbaum, Henry; Strawich, Elsa; Graham, Lila; Rey, Christian; Chiu, Hank; Müller, Ralph; Hashemi, Hamid Nayeb; Vaziri, Ashkan; Nazarian, Ara

    2015-01-01

    The aim of this study was to explore the hierarchical arrangement of structural properties in cortical and trabecular bone and to determine a mathematical model that accurately predicts the tissue's mechanical properties as a function of these indices. By using a variety of analytical techniques, we were able to characterize the structural and compositional properties of cortical and trabecular bones, as well as to determine the suitable mathematical model to predict the tissue's mechanical properties using a continuum micromechanics approach. Our hierarchical analysis demonstrated that the differences between cortical and trabecular bone reside mainly at the micro- and ultrastructural levels. By gaining a better appreciation of the similarities and differences between the two bone types, we would be able to provide a better assessment and understanding of their individual roles, as well as their contribution to bone health overall. PMID:25808343

  5. Multi-scale model for point defects behaviour in uranium mononitride

    NASA Astrophysics Data System (ADS)

    Starikov, S.; Kuksin, A.; Smirnova, D.

    2017-01-01

    A multiscale approach was used to study the properties of point defects in uranium mononitride (UN). In this work we used combination of several methods: ab initio calculations; molecular dynamics simulations with a new interatomic potential; thermodynamic model. Density functional theory (DFT) calculations are used for fitting of the parameters of the angular-dependent interatomic potential, as well as for evaluation of the defects formation and migration energies. Molecular dynamics (MD) simulations are applied to analyze what migration/formation mechanisms are activated at finite temperatures and to calculate diffusion coefficients of point defects. The thermodynamic model for description of concentrations and diffusivities for point defects in non-stoichiometric UN1+x is proposed.

  6. Multi-scale Modeling of Energy Balance Fluxes in a Dense Tamarisk Riparian Forest

    NASA Astrophysics Data System (ADS)

    Neale, C. M.; Santos, C. A.; Watts, D.; Osterberg, J.; Hipps, L. E.; Sritharan, S. I.

    2008-12-01

    Remote sensing of energy balance fluxes has become operationally more viable over the last 10 years with the development of more robust multi-layer models and the availability of quasi-real time satellite imagery from most sensors. Riparian corridors in semi-arid and arid areas present a challenge to satellite based techniques for estimating evapotranspiration due to issues of scale and pixel resolution, especially when using the thermal infrared bands. This paper will present energy balance measurement and modeling results over a Salt Cedar (Tamarix Ramosissima) forest in the Cibola National Wildlife Refuge along the Colorado River south of Blythe, CA. The research site encompasses a 600 hectare area populated by mostly Tamarisk stands of varying density. Three Bowen ratio systems are installed on tall towers within varying densities of forest cover in the upwind footprint and growing under varying depths to the water table. An additional eddy covariance tower is installed alongside a Bowen ratio system on one of the towers. Flux data has been gathered continuously since early 2007. In the summer of 2007, a Scintec large aperture scintillometer was installed between two of the towers over 1 km apart and has been working continuously along with the flux towers. Two intensive field campaigns were organized in June 2007 and May 2008 to coincide with LANDSAT TM5, MODIS and ASTER overpasses. High resolution multispectral and thermal imagery was acquired at the same time with the USU airborne system to provide information for the up- scaling of the energy balance fluxes from tower to satellite scales. The paper will present comparisons between the different energy balance measuring techniques under the highly advective conditions of the experimental site, concentrating on the scintillometer data. Preliminary results of remotely sensed modeling of the fluxes at different scales and model complexity will also be presented.

  7. A multi-scale conceptual model of fire and disease interactions in North American forests

    NASA Astrophysics Data System (ADS)

    Varner, J. M.; Kreye, J. K.; Sherriff, R.; Metz, M.

    2013-12-01

    One aspect of global change with increasing attention is the interactions between irruptive pests and diseases and wildland fire behavior and effects. These pests and diseases affect fire behavior and effects in spatially and temporally complex ways. Models of fire and pathogen interactions have been constructed for individual pests or diseases, but to date, no synthesis of this complexity has been attempted. Here we synthesize North American fire-pathogen interactions into syndromes with similarities in spatial extent and temporal duration. We base our models on fire interactions with three examples: sudden oak death (caused by the pathogen Phytopthora ramorum) and the native tree tanoak (Notholithocarpus densiflorus); mountain pine beetle (Dendroctonus ponderosae) and western Pinus spp.; and hemlock woolly adelgid (Adelges tsugae) on Tsuga spp. We evaluate each across spatial (severity of attack from branch to landscape scale) and temporal scales (from attack to decades after) and link each change to its coincident effects on fuels and potential fire behavior. These syndromes differ in their spatial and temporal severity, differentially affecting windows of increased or decreased community flammability. We evaluate these models with two examples: the recently emergent ambrosia beetle-vectored laurel wilt (caused by the pathogen Raffaelea lauricola) in native members of the Lauraceae and the early 20th century chestnut blight (caused by the pathogen Cryphonectria parasitica) that led to the decline of American chestnut (Castanea dentata). Some changes (e.g., reduced foliar moisture content) have short-term consequences for potential fire behavior while others (functional extirpation) have more complex indirect effects on community flammability. As non-native emergent diseases and pests continue, synthetic models that aid in prediction of fire behavior and effects will enable the research and management community to prioritize mitigation efforts to realized effects.

  8. Multi-scale and Multi-physics Numerical Methods for Modeling Transport in Mesoscopic Systems

    DTIC Science & Technology

    2014-10-13

    Triangle Park, NC 27709-2211 Transport, Electromagnetic Phenomena, nano-electronics, ion channels , layered media REPORT DOCUMENTATION PAGE 11. SPONSOR...DFT for quantum systems. (3) numerical methods for computation of electrostatics in ion- channel transport, (4) a new parallel solver for elliptic...10.00 Received Paper 9.00 Huimin Lin, Huazhong Tang, Wei Cai. Accuracy and efficiency in computing electrostatic potentialfor an ion channel model in

  9. Stress distribution retrieval in granular materials: A multi-scale model and digital image correlation measurements

    NASA Astrophysics Data System (ADS)

    Bruno, Luigi; Decuzzi, Paolo; Gentile, Francesco

    2016-01-01

    The promise of nanotechnology lies in the possibility of engineering matter on the nanoscale and creating technological interfaces that, because of their small scales, may directly interact with biological objects, creating new strategies for the treatment of pathologies that are otherwise beyond the reach of conventional medicine. Nanotechnology is inherently a multiscale, multiphenomena challenge. Fundamental understanding and highly accurate predictive methods are critical to successful manufacturing of nanostructured materials, bio/mechanical devices and systems. In biomedical engineering, and in the mechanical analysis of biological tissues, classical continuum approaches are routinely utilized, even if these disregard the discrete nature of tissues, that are an interpenetrating network of a matrix (the extra cellular matrix, ECM) and a generally large but finite number of cells with a size falling in the micrometer range. Here, we introduce a nano-mechanical theory that accounts for the-non continuum nature of bio systems and other discrete systems. This discrete field theory, doublet mechanics (DM), is a technique to model the mechanical behavior of materials over multiple scales, ranging from some millimeters down to few nanometers. In the paper, we use this theory to predict the response of a granular material to an external applied load. Such a representation is extremely attractive in modeling biological tissues which may be considered as a spatial set of a large number of particulate (cells) dispersed in an extracellular matrix. Possibly more important of this, using digital image correlation (DIC) optical methods, we provide an experimental verification of the model.

  10. Multi-scale hybrid models for radiopharmaceutical dosimetry with Geant4.

    PubMed

    Marcatili, S; Villoing, D; Garcia, M P; Bardiès, M

    2014-12-21

    The accuracy of radiopharmaceutical absorbed dose distributions computed through Monte Carlo (MC) simulations is mostly limited by the low spatial resolution of 3D imaging techniques used to define the simulation geometry. This issue also persists with the implementation of realistic hybrid models built using polygonal mesh and/or NURBS as they require to be simulated in their voxel form in order to reduce computation times. The existing trade-off between voxel size and simulation speed leads on one side, in an overestimation of the size of small radiosensitive structures such as the skin or hollow organs walls and, on the other, to unnecessarily detailed voxelization of large, homogeneous structures.We developed a set of computational tools based on VTK and Geant4 in order to build multi-resolution organ models. Our aim is to use different voxel sizes to represent anatomical regions of different clinical relevance: the MC implementation of these models is expected to improve spatial resolution in specific anatomical structures without significantly affecting simulation speed. Here we present the tools developed through a proof of principle example. Our approach is validated against the standard Geant4 technique for the simulation of voxel geometries.

  11. Multi-Scale Modeling of Respiration: Linking External to Cellular Respiration during Exercise

    PubMed Central

    Zhou, Haiying; Lai, Nicola; Saidel, Gerald M.; Cabrera, Marco E.

    2014-01-01

    In human studies investigating factors that control cellular respiration in working skeletal muscle, pulmonary VO2 dynamics (VO2p) measured at the mouth by indirect calorimetry is typically used to represent muscle O2 consumption (UO2m). Furthermore, measurement of muscle oxygenation using near-infrared spectroscopy has provided information on the dynamic balance between oxygen delivery and oxygen consumption at the microvascular level. To relate these measurements and gain quantitative understanding of the regulation of VO2 at the cellular, tissue and whole-body level, a multiscale computational model of oxygen transport and metabolism during exercise was developed. The model incorporates mechanisms of oxygen transport from the airway opening to working muscle and other-organs cells, as well as the phosphagenic and oxidative pathways of ATP synthesis in these tissue cells. Model simulations of external (VO2p) and cellular (UO2m) respiration show that, during moderate exercise, their characteristic mean response times are similar even when a transit delay exists between tissue cells and the external environment for normal subjects. PMID:19457732

  12. A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation

    PubMed Central

    Hester, Susan D.; Belmonte, Julio M.; Gens, J. Scott; Clendenon, Sherry G.; Glazier, James A.

    2011-01-01

    Somitogenesis, the formation of the body's primary segmental structure common to all vertebrate development, requires coordination between biological mechanisms at several scales. Explaining how these mechanisms interact across scales and how events are coordinated in space and time is necessary for a complete understanding of somitogenesis and its evolutionary flexibility. So far, mechanisms of somitogenesis have been studied independently. To test the consistency, integrability and combined explanatory power of current prevailing hypotheses, we built an integrated clock-and-wavefront model including submodels of the intracellular segmentation clock, intercellular segmentation-clock coupling via Delta/Notch signaling, an FGF8 determination front, delayed differentiation, clock-wavefront readout, and differential-cell-cell-adhesion-driven cell sorting. We identify inconsistencies between existing submodels and gaps in the current understanding of somitogenesis mechanisms, and propose novel submodels and extensions of existing submodels where necessary. For reasonable initial conditions, 2D simulations of our model robustly generate spatially and temporally regular somites, realistic dynamic morphologies and spontaneous emergence of anterior-traveling stripes of Lfng. We show that these traveling stripes are pseudo-waves rather than true propagating waves. Our model is flexible enough to generate interspecies-like variation in somite size in response to changes in the PSM growth rate and segmentation-clock period, and in the number and width of Lfng stripes in response to changes in the PSM growth rate, segmentation-clock period and PSM length. PMID:21998560

  13. Multi-scale occupancy estimation and modelling using multiple detection methods

    USGS Publications Warehouse

    Nichols, James D.; Bailey, Larissa L.; O'Connell, Allan F.; Talancy, Neil W.; Grant, Evan H. Campbell; Gilbert, Andrew T.; Annand, Elizabeth M.; Husband, Thomas P.; Hines, James E.

    2008-01-01

    Occupancy estimation and modelling based on detection–nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method.We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species’ use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site.We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber. For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species.Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can be

  14. Multi-scale modeling of photopolymerization for medical hydrogel-implant design

    NASA Astrophysics Data System (ADS)

    Schmocker, Andreas; Khoushabi, Azadeh; Farahi, Salma; Pioletti, Dominique; Bourban, Pierre-Etienne; Manson, Jan A.; Moser, Christophe

    2013-02-01

    We report on the modeling of a photopolymerizable hydrogel and its application as a replacement of the interior of the intervertebral disc (so called Nucleus Pulposus). The hydrogel is initially injected in its liquid form and then photopolymerized via a small catheter. Therefore, also the light necessary for the photopolymerization is constrained to a small light guide to keep the surgical procedure as minimally invasive as possible. Hence, the hydrogel is photopolymerized inside. For applications with restricted physical access and illumination time, such as an Nucleus Pulposus replacement, photopolymerization of volumes with a large volume/illumination-area ratio becomes highly challenging. During polymerization, the material's absorption and scattering coefficients change and directly influence local polymerization rates. By understanding and controlling such polymerization patterns, local material properties can be engineered (e.g. elastic modulus, swelling ratio), to match the set of mechanical requirements for the implant. Thus, it is essential to better understand and model photopolymerization reactions. Experiments were conducted by polymerizing a hydrogel in a column-like volume using an optical fiber for light delivery. Quantitative scattering and absorption values as well as monomer conversion rates of the hydrogel sample were validated using a newly established Monte Carlo model for photopolymerization. The results were used to study and predict 3D polymerization patterns for different illumination configurations. In particular, we show an example of a lumbar intervertebral disc replacement where the jelly core of the intervertebral disc (Nucleus Pulposus) is replaced by an in situ photopolymerized hydrogel. The results provide insights for the development of novel endoscopic light-scattering polymerization probes paving the way for a new generation of implantable hydrogels.

  15. HydroSCAPE: a multi-scale framework for streamflow routing in large-scale hydrological models

    NASA Astrophysics Data System (ADS)

    Piccolroaz, S.; Di Lazzaro, M.; Zarlenga, A.; Majone, B.; Bellin, A.; Fiori, A.

    2015-09-01

    We present HydroSCAPE, a large scale hydrological model with an innovative streamflow routing scheme based on the Width Function Instantaneous Unit Hydrograph (WFIUH) theory, which is designed to facilitate coupling with weather forecasting and climate models. HydroSCAPE preserves geomorphological dispersion of the river network when dealing with horizontal hydrological fluxes, irrespective of the adopted grid size, which is typically inherited from the overlaying weather forecast or climate model. This is achieved through a separate treatment of hillslope processes and routing within the river network, with the latter simulated by suitable transfer functions constructed by applying the WFIUH theory to the desired level of detail. Transfer functions are constructed for each grid cell and nodes of the network where water discharge is desired by taking advantage of the detailed morphological information contained in the Digital Elevation Model of the zone of interest. These characteristics render HydroSCAPE well suited for multi-scale applications, ranging from catchment up to continental scale, and to investigate extreme events (e.g. floods) that require an accurate description of routing through the river network. The model enjoys reliability and robustness, united to parsimony in the adopted parametrization and computational efficiency, leading to a dramatic reduction of the computational effort with respect to full-gridded models at comparable level of accuracy of routing. Additionally, HydroSCAPE is designed with a simple and flexible modular structure, which makes it particularly suitable to massive parallelization, customization according to the specific user needs and preferences (e.g. choice of rainfall-runoff model), and continuous development and improvements.

  16. Multi-Scale Modeling of Novel Hall Thrusters: Understanding Physics of CHT and DCF Thrusters

    DTIC Science & Technology

    2011-12-30

    and ions in a general 2D domain (or 3D) and a 1D kinetic full PIC treatment of electrons along magnetic fields. The implementation of such a two-way...general 2D domain (or 3D) and a 1D kinetic full PIC treatment of electrons along magnetic fields. The implementation of such a two-way coupling allows...modeled as a quasi- 1D fluid. Quasineutrality is assumed, and the kinetically determined plasma density is used to update the electron temperature in

  17. Multi-scale coupling strategy for fully two-dimensional and depth-averaged models for granular flows

    NASA Astrophysics Data System (ADS)

    Pudasaini, Shiva P.; Domnik, Birte; Miller, Stephen A.

    2013-04-01

    We developed a full two-dimensional Coulomb-viscoplastic model and applied it for inclined channel flows of granular materials from initiation to their deposition. The model includes the basic features and observed phenomena in dense granular flows like the exhibition of a yield strength and a non-zero slip velocity. A pressure-dependent yield strength is proposed to account for the frictional nature of granular materials. The yield strength can be related to the internal friction angle of the material and plays an important role, for example, in deposition processes. The interaction of the flow with the solid boundary is modelled by a pressure and rate-dependent Coulomb-viscoplastic sliding law. We developed an innovative multi-scale strategy to couple the full two-dimensional, non depth-averaged model (N-DAM) with a one-dimensional, depth-averaged model (DAM). The coupled model reduces computational complexity dramatically by using DAM only in regions with smooth changes of flow variables. The numerics uses N-DAM in regions where depth-averaging becomes inaccurate, for instance, in the initiation and deposition regions, and (particularly) when the flow hits an obstacle or a defense structure. In these regions, momentum transfer must be, and is, considered in all directions. We observe very high coupling performance, and show that the numerical results deviate only slightly from results of the much more cumbersome full two-dimensional model. This shows that the coupled model, which retains all the basic physics of the flow, is an attractive alternative to an expensive, full two-dimensional simulations. We compare simulation results with different experimental data for shock waves appearing in rapid granular flows down inclined channels and impacting a wall. The model predicts the evolution of the strong shock wave and the impact force on a rigid wall for different inclination angles and sliding surfaces. It is demonstrated that the internal friction angle plays an

  18. New insights into chromatin folding and dynamics from multi-scale modeling

    NASA Astrophysics Data System (ADS)

    Olson, Wilma

    The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes-the familiar assemblies of roughly 150 DNA base pairs and eight histone proteins-found on chromatin fibers. We have developed a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs with 3-25 evenly spaced nucleosomes. The correspondence between the predicted and observed effects of nucleosome composition, spacing, and numbers on long-range communication between regulatory proteins bound to the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We have extracted effective nucleosome-nucleosome potentials from the mesoscale simulations and introduced the potentials in a larger scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable influence of nucleosome spacing on chromatin flexibility. Small changes in the length of the DNA fragments linking successive nucleosomes introduce marked changes in the local interactions of the nucleosomes and in the spatial configurations of the fiber as a whole. The changes in nucleosome positioning influence the statistical properties of longer chromatin constructs with 100-10,000 nucleosomes. We are investigating the extent to which the `local' interactions of regularly spaced nucleosomes contribute to the corresponding interactions in chains with mixed spacings as a step toward the treatment of fibers with nucleosomes positioned at the sites mapped at base-pair resolution on genomic sequences. Support of the work by USPHS R01 GM 34809 is gratefully acknowledged.

  19. The phase behavior study of human antibody solution using multi-scale modeling

    NASA Astrophysics Data System (ADS)

    Sun, Gang; Wang, Ying; Lomakin, Aleksey; Benedek, George B.; Stanley, H. Eugene; Xu, Limei; Buldyrev, Sergey V.

    2016-11-01

    Phase transformation in antibody solutions is of growing interest in both academia and the pharmaceutical industry. Recent experimental studies have shown that, as in near-spherical proteins, antibodies can undergo a liquid-liquid phase separation under conditions metastable with respect to crystallization. However, the phase diagram of the Y-shaped antibodies exhibits unique features that differ substantially from those of spherical proteins. Specifically, antibody solutions have an exceptionally low critical volume fraction (CVF) and a broader and more asymmetric liquid-liquid coexistence curve than those of spherical proteins. Using molecular dynamics simulation on a series of trimetric Y-shaped coarse-grained models, we investigate the phase behavior of antibody solutions and compare the results with the experimental phase diagram of human immunoglobulin G (IgG), one of the most common Y-shape typical of antibody molecules. With the fitted size of spheres, our simulation reproduces both the low CVF and the asymmetric shape of the experimental coexistence curve of IgG antibodies. The broadness of the coexistence curve can be attributed to the anisotropic nature of the inter-protein interaction. In addition, the repulsion between the inner parts of the spherical domains of IgG dramatically expands the coexistence region in the scaled phase diagram, while the hinge length has only a minor effect on the CVF and the overall shape of the coexistence curve. We thus propose a seven-site model with empirical parameters characterizing the exclusion volume and the hinge length of the IgG molecules, which provides a base for simulation studies of the phase behavior of IgG antibodies.

  20. Investigation of urban faults in Shenzhen using wavelet multi-scale analysis and modeling of gravity observations

    NASA Astrophysics Data System (ADS)

    Xu, Chuang; Chen, Liang; Liu, Xi-kai

    2016-04-01

    Urban faults in Shenzhen are potential threat to the city security and sustainable development. To improve the knowledge of the Shenzhen fault zone, interpretation and inversion of gravity data were carried out. Bouguer gravity covering the whole Shenzhen city was calculated with a resolution of 1kmx1km. Wavelet multi-scale analysis (MSA) was applied to the Bouguer gravity data to obtain the multilayer residual anomalies corresponding to different depths. In addition, 2D gravity models were constructed along three profiles. The Bouguer gravity anomaly shows a NE-striking high-low-high pattern from northwest to southeast, strongly related to the main faults. According to the result of MSA, the correlation between gravity anomaly and faults is particularly significant from 4 to 12 km depth. The residual gravity with small amplitude in each layer indicates weak tectonic activity in the crust. In the upper layers, positive anomalies along most of faults reveal the upwelling of high-density materials during the past tectonic movements. The multilayer residual anomalies also implicate important information about the faults, such as the vertical extension and the dip direction. The maximum depth of the faults is about 20km. In general, NE-striking faults extend deeper than NW-striking Faults and have a larger dip angle. This study is supported by the National Natural Science Foundation of China (Grant No.41504015) and China Postdoctoral Science Foundation (Grant No.2015M572146).

  1. Segmentation of pelvic structures for planning CT using a geometrical shape model tuned by a multi-scale edge detector

    PubMed Central

    Martínez, Fabio; Romero, Eduardo; Dréan, Gaël; Simon, Antoine; Haigron, Pascal; De Crevoisier, Renaud; Acosta, Oscar

    2014-01-01

    Accurate segmentation of the prostate and organs at risk in computed tomography (CT) images is a crucial step for radiotherapy (RT) planning. Manual segmentation, as performed nowadays, is a time consuming process and prone to errors due to the a high intra- and inter-expert variability. This paper introduces a new automatic method for prostate, rectum and bladder segmentation in planning CT using a geometrical shape model under a Bayesian framework. A set of prior organ shapes are first built by applying Principal Component Analysis (PCA) to a population of manually delineated CT images. Then, for a given individual, the most similar shape is obtained by mapping a set of multi-scale edge observations to the space of organs with a customized likelihood function. Finally, the selected shape is locally deformed to adjust the edges of each organ. Experiments were performed with real data from a population of 116 patients treated for prostate cancer. The data set was split in training and test groups, with 30 and 86 patients, respectively. Results show that the method produces competitive segmentations w.r.t standard methods (Averaged Dice = 0.91 for prostate, 0.94 for bladder, 0.89 for Rectum) and outperforms the majority-vote multi-atlas approaches (using rigid registration, free-form deformation (FFD) and the demons algorithm) PMID:24594798

  2. Segmentation of pelvic structures for planning CT using a geometrical shape model tuned by a multi-scale edge detector

    NASA Astrophysics Data System (ADS)

    Martínez, Fabio; Romero, Eduardo; Dréan, Gaël; Simon, Antoine; Haigron, Pascal; de Crevoisier, Renaud; Acosta, Oscar

    2014-03-01

    Accurate segmentation of the prostate and organs at risk in computed tomography (CT) images is a crucial step for radiotherapy planning. Manual segmentation, as performed nowadays, is a time consuming process and prone to errors due to the a high intra- and inter-expert variability. This paper introduces a new automatic method for prostate, rectum and bladder segmentation in planning CT using a geometrical shape model under a Bayesian framework. A set of prior organ shapes are first built by applying principal component analysis to a population of manually delineated CT images. Then, for a given individual, the most similar shape is obtained by mapping a set of multi-scale edge observations to the space of organs with a customized likelihood function. Finally, the selected shape is locally deformed to adjust the edges of each organ. Experiments were performed with real data from a population of 116 patients treated for prostate cancer. The data set was split in training and test groups, with 30 and 86 patients, respectively. Results show that the method produces competitive segmentations w.r.t standard methods (averaged dice = 0.91 for prostate, 0.94 for bladder, 0.89 for rectum) and outperforms the majority-vote multi-atlas approaches (using rigid registration, free-form deformation and the demons algorithm).

  3. Multi-scale model of drug induced adaptive resistance of Gram-negative bacteria to polymyxin B

    PubMed Central

    Krzyzanski, Wojciech

    2017-01-01

    The purpose of this report is to apply multi-scale modeling using the theory of physiologically structured populations (PSP) to develop a mathematical model for antimicrobial resistance based on a heterogeneous distribution of receptors and affinities among bacterial cells. The theory has been tested on data obtained from an in vitro static time-kill infection model analyzing the pharmacodynamics of polymyxin B against Gram-negative bacteria. The drug binding parameter KD (dissociation equilibrium constant) is assumed to vary between the bacterial cells. The PSP model describes the time course of the density distribution of KD upon exposure to cytotoxic drug concentrations. The drug increases the hazard of cell death as a function of receptor occupancy. The initial distribution of KD is described by the Weibull function. Time-kill data were used for model qualification. In vitro static time-kill experiments to evaluate the rate and extent of killing due to polymyxin B against two Klebsiella pneumoniae clinical isolates with differing susceptibilities to polymyxin B were performed over 48 h. The time-kill kinetics data of bacterial load cfu (colony forming units)/mL was used for model qualification. The resistant bacterial population is determined by the balance between growth rate and hazard of cell death controlled by polymyxin B concentrations. There exists a critical KD value below which cells continue to grow. Estimates of shape parameters for distributions of KD yielded unimodal distributions with the modes at 0 nM and the right tails containing approximately 25% of the bacteria. Our findings support a hypothesis that resistance of Klebsiella pneumoniae to polymyxin B can be at least partially attributed to a drug-induced selection of a subpopulation due to heterogeneity of polymyxin B receptor binding in the bacterial population. PMID:28334005

  4. Impact of spatial data resolution on simulated catchment water balances and model performance of the multi-scale TOPLATS model

    NASA Astrophysics Data System (ADS)

    Bormann, H.

    2006-03-01

    This paper analyses the effect of spatial input data resolution on the simulated water balances and flow components using the multi-scale hydrological model TOPLATS. A data set of 25m resolution of the central German Dill catchment (693 km2) is used for investigation. After an aggregation of digital elevation model, soil map and land use classification to 50 m, 75 m, 100 m, 150 m, 200 m, 300 m, 500 m, 1000 m and 2000 m, water balances and water flow components are calculated for the entire Dill catchment as well as for 3 subcatchments without any recalibration. The study shows that model performance measures and simulated water balances almost remain constant for most of the aggregation steps for all investigated catchments. Slight differences in the simulated water balances and statistical quality measures occur for single catchments at the resolution of 50 m to 500 m (e.g. 0-3% for annual stream flow), significant differences at the resolution of 1000 m and 2000 m (e.g. 2-12% for annual stream flow). These differences can be explained by the fact that the statistics of certain input data (land use data in particular as well as soil physical characteristics) changes significantly at these spatial resolutions. The impact of smoothing the relief by aggregation occurs continuously but is barely reflected by the simulation results. To study the effect of aggregation of land use data in detail, in addition to current land use the effect of aggregation on the water balance calculations based on three different land use scenarios is investigated. Land use scenarios were available aiming on economic optimisation of agricultural and forestry practices at different field sizes (0.5 ha, 1.5 ha and 5.0 ha). The changes in water balance terms, induced by aggregation of the land use scenarios, are comparable with respect to catchment water balances compared to the current land use. A correlation analysis between statistics of input data and simulated annual water fluxes only in

  5. Multi-scale modeling of CO2 dispersion leaked from seafloor off the Japanese coast.

    PubMed

    Kano, Yuki; Sato, Toru; Kita, Jun; Hirabayashi, Shinichiro; Tabeta, Shigeru

    2010-02-01

    A numerical simulation was conducted to predict the change of pCO(2) in the ocean caused by CO(2) leaked from an underground aquifer, in which CO(2) is purposefully stored. The target space of the present model was the ocean above the seafloor. The behavior of CO(2) bubbles, their dissolution, and the advection-diffusion of dissolved CO(2) were numerically simulated. Here, two cases for the leakage rate were studied: an extreme case, 94,600 t/y, which assumed that a large fault accidentally connects the CO(2) reservoir and the seafloor; and a reasonable case, 3800 t/y, based on the seepage rate of an existing EOR site. In the extreme case, the calculated increase in DeltapCO(2) experienced by floating organisms was less than 300 ppm, while that for immobile organisms directly over the fault surface periodically exceeded 1000 ppm, if momentarily. In the reasonable case, the calculated DeltapCO(2) and pH were within the range of natural fluctuation.

  6. Probabilistic Downscaling of Remote Sensing Data with Applications for Multi-Scale Biogeochemical Flux Modeling

    PubMed Central

    Stoy, Paul C.; Quaife, Tristan

    2015-01-01

    Upscaling ecological information to larger scales in space and downscaling remote sensing observations or model simulations to finer scales remain grand challenges in Earth system science. Downscaling often involves inferring subgrid information from coarse-scale data, and such ill-posed problems are classically addressed using regularization. Here, we apply two-dimensional Tikhonov Regularization (2DTR) to simulate subgrid surface patterns for ecological applications. Specifically, we test the ability of 2DTR to simulate the spatial statistics of high-resolution (4 m) remote sensing observations of the normalized difference vegetation index (NDVI) in a tundra landscape. We find that the 2DTR approach as applied here can capture the major mode of spatial variability of the high-resolution information, but not multiple modes of spatial variability, and that the Lagrange multiplier (γ) used to impose the condition of smoothness across space is related to the range of the experimental semivariogram. We used observed and 2DTR-simulated maps of NDVI to estimate landscape-level leaf area index (LAI) and gross primary productivity (GPP). NDVI maps simulated using a γ value that approximates the range of observed NDVI result in a landscape-level GPP estimate that differs by ca 2% from those created using observed NDVI. Following findings that GPP per unit LAI is lower near vegetation patch edges, we simulated vegetation patch edges using multiple approaches and found that simulated GPP declined by up to 12% as a result. 2DTR can generate random landscapes rapidly and can be applied to disaggregate ecological information and compare of spatial observations against simulated landscapes. PMID:26067835

  7. Probabilistic Downscaling of Remote Sensing Data with Applications for Multi-Scale Biogeochemical Flux Modeling.

    PubMed

    Stoy, Paul C; Quaife, Tristan

    2015-01-01

    Upscaling ecological information to larger scales in space and downscaling remote sensing observations or model simulations to finer scales remain grand challenges in Earth system science. Downscaling often involves inferring subgrid information from coarse-scale data, and such ill-posed problems are classically addressed using regularization. Here, we apply two-dimensional Tikhonov Regularization (2DTR) to simulate subgrid surface patterns for ecological applications. Specifically, we test the ability of 2DTR to simulate the spatial statistics of high-resolution (4 m) remote sensing observations of the normalized difference vegetation index (NDVI) in a tundra landscape. We find that the 2DTR approach as applied here can capture the major mode of spatial variability of the high-resolution information, but not multiple modes of spatial variability, and that the Lagrange multiplier (γ) used to impose the condition of smoothness across space is related to the range of the experimental semivariogram. We used observed and 2DTR-simulated maps of NDVI to estimate landscape-level leaf area index (LAI) and gross primary productivity (GPP). NDVI maps simulated using a γ value that approximates the range of observed NDVI result in a landscape-level GPP estimate that differs by ca 2% from those created using observed NDVI. Following findings that GPP per unit LAI is lower near vegetation patch edges, we simulated vegetation patch edges using multiple approaches and found that simulated GPP declined by up to 12% as a result. 2DTR can generate random landscapes rapidly and can be applied to disaggregate ecological information and compare of spatial observations against simulated landscapes.

  8. Multi-scale finite element model of growth plate damage during the development of slipped capital femoral epiphysis.

    PubMed

    Farzaneh, S; Paseta, O; Gómez-Benito, M J

    2015-04-01

    Slipped capital femoral epiphysis (SCFE) is one of the most common disorders of adolescent hips. A number of works have related the development of SCFE to mechanical factors. Due to the difficulty of diagnosing SCFE in its early stages, the disorder often progresses over time, resulting in serious side effects. Therefore, the development of a tool to predict the initiation of damage in the growth plate is needed. Because the growth plate is a heterogeneous structure, to develop a precise and reliable model, it is necessary to consider this structure from both macro- and microscale perspectives. Thus, the main objective of this work is to develop a numerical multi-scale model that links damage occurring at the microscale to damage occurring at the macroscale. The use of this model enables us to predict which regions of the growth plate are at high risk of damage. First, we have independently analyzed the microscale to simulate the microstructure under shear and tensile tests to calibrate the damage model. Second, we have employed the model to simulate damage occurring in standardized healthy and affected femurs during the heel-strike stage of stair climbing. Our results indicate that on the macroscale, damage is concentrated in the medial region of the growth plate in both healthy and affected femurs. Furthermore, damage to the affected femur is greater than damage to the healthy femur from both the micro- and macrostandpoints. Maximal damage is observed in territorial matrices. Furthermore, simulations illustrate that little damage occurs in the reserve zone. These findings are consistent with previous findings reported in well-known experimental works.

  9. Global net land carbon sink: Results from the Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP)

    NASA Astrophysics Data System (ADS)

    Huntzinger, D. N.; Schwalm, C. R.; Michalak, A. M.; Cook, R. B.; Jacobson, A. R.; Schaefer, K. M.; Dasgupta, A.; Poco, J.

    2013-12-01

    The Multi-scale Synthesis and Model Intercomparison Project (MsTMIP) is a formal model intercomparison effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. Here we present results from the terrestrial biospheric models participating in the MsTMIP effort, focusing on global and regional model estimates of the net land carbon sink. When compared to estimates of the residual net land sink inferred from atmospheric CO2 observations (i.e., fossil fuel emission + land use land cover change - atmospheric increase - ocean uptake), MsTMIP models predict, on average, a weaker global net land uptake of carbon. There is a large spread in MsTMIP estimates of the net land sink (e.g., -2.5 to 5.0 Pg C/yr in 2010, where a negative flux represents a net release to the atmosphere). Some models consistently show the land surface as a net source of carbon to the atmosphere, which is inconsistent with the atmospheric record. In addition, we examine how model estimates of the cumulative global net sink diverge over the period 1900 to 2010, and the degree to which model sensitivity to forcing factors and fundamental differences in model formulation contribute to this divergence. We link differences in estimates of the cumulative land sink back to each model's sensitivity to key forcing factors including climate variability, CO2 fertilization, nitrogen limitation, and land cover / land-use change. For example, the strength of carbon uptake in most models appears to be strongly coupled with atmospheric CO2 concentrations (CO2 fertilization effect). The strength of this relationship, however, varies across models with some models exhibiting a very strong CO2 fertilization effect (e.g., ORCHIDEE), while others not so (e.g., CLM). To inform the comparison across models, structural differences (i.e., which processes are included and how those processes are parameterized) among the participating models are evaluated using hierarchical

  10. Multi-scale computational models of the airways to unravel the pathophysiological mechanisms in asthma and chronic obstructive pulmonary disease (AirPROM)

    PubMed Central

    Burrowes, K. S.; De Backer, J.; Smallwood, R.; Sterk, P. J.; Gut, I.; Wirix-Speetjens, R.; Siddiqui, S.; Owers-Bradley, J.; Wild, J.; Maier, D.; Brightling, C.

    2013-01-01

    The respiratory system comprises several scales of biological complexity: the genes, cells and tissues that work in concert to generate resultant function. Malfunctions of the structure or function of components at any spatial scale can result in diseases, to the detriment of gas exchange, right heart function and patient quality of life. Vast amounts of data emerge from studies across each of the biological scales; however, the question remains: how can we integrate and interpret these data in a meaningful way? Respiratory disease presents a huge health and economic burden, with the diseases asthma and chronic obstructive pulmonary disease (COPD) affecting over 500 million people worldwide. Current therapies are inadequate owing to our incomplete understanding of the disease pathophysiology and our lack of recognition of the enormous disease heterogeneity: we need to characterize this heterogeneity on a patient-specific basis to advance healthcare. In an effort to achieve this goal, the AirPROM consortium (Airway disease Predicting Outcomes through patient-specific computational Modelling) brings together a multi-disciplinary team and a wealth of clinical data. Together we are developing an integrated multi-scale model of the airways in order to unravel the complex pathophysiological mechanisms occurring in the diseases asthma and COPD. PMID:24427517

  11. Multi-scale Characterization and Modeling of Surface Slope Probability Distribution for ~20-km Diameter Lunar Craters

    NASA Astrophysics Data System (ADS)

    Mahanti, P.; Robinson, M. S.; Boyd, A. K.

    2013-12-01

    Craters ~20-km diameter and above significantly shaped the lunar landscape. The statistical nature of the slope distribution on their walls and floors dominate the overall slope distribution statistics for the lunar surface. Slope statistics are inherently useful for characterizing the current topography of the surface, determining accurate photometric and surface scattering properties, and in defining lunar surface trafficability [1-4]. Earlier experimental studies on the statistical nature of lunar surface slopes were restricted either by resolution limits (Apollo era photogrammetric studies) or by model error considerations (photoclinometric and radar scattering studies) where the true nature of slope probability distribution was not discernible at baselines smaller than a kilometer[2,3,5]. Accordingly, historical modeling of lunar surface slopes probability distributions for applications such as in scattering theory development or rover traversability assessment is more general in nature (use of simple statistical models such as the Gaussian distribution[1,2,5,6]). With the advent of high resolution, high precision topographic models of the Moon[7,8], slopes in lunar craters can now be obtained at baselines as low as 6-meters allowing unprecedented multi-scale (multiple baselines) modeling possibilities for slope probability distributions. Topographic analysis (Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) 2-m digital elevation models (DEM)) of ~20-km diameter Copernican lunar craters revealed generally steep slopes on interior walls (30° to 36°, locally exceeding 40°) over 15-meter baselines[9]. In this work, we extend the analysis from a probability distribution modeling point-of-view with NAC DEMs to characterize the slope statistics for the floors and walls for the same ~20-km Copernican lunar craters. The difference in slope standard deviations between the Gaussian approximation and the actual distribution (2-meter sampling) was

  12. Using Multi-scale Modeling System to Study the Interactions between Clouds, Precipitation, Aerosols, Radiation and Land Surface

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2006-01-01

    nesting technique. A review of developments, improvements and applications of cloud models (GCE and WRF) at Goddard will be presented in this talk. In particular, a new approach to using multi-scale modeling system to study the interactions between clouds, precipitation, aerosols and land will be presented.

  13. Using Multi-scale Modeling System to Study the Interactions between Clouds, Precipitation, Aerosols, Radiation and Land Surface

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2006-01-01

    technique. A review of developments, improvements and applications of cloud models (GCE and WRF) at Goddard wlll be is presented in this talk. In particular, a new approach to using multi-scale modeling system to study the interactions between clouds, precipitation, aerosols and land will be presented.

  14. Using Multi-scale Modeling System to Study the Interactions between Clouds, Precipitation, Aerosols, Radiation and Land Surface

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo

    2006-01-01

    developments, improvements and applications of cloud models (GCE and WRF) at Goddard will be presented in this talk. In particular, a new approach to using multi-scale modeling system to study the interactions between clouds, precipitation, aerosols and land will be presented.

  15. Stochastic multi-scale models of competition within heterogeneous cellular populations: Simulation methods and mean-field analysis.

    PubMed

    Cruz, Roberto de la; Guerrero, Pilar; Spill, Fabian; Alarcón, Tomás

    2016-10-21

    We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated proliferation rate. Our formulation is based on an age-dependent stochastic process. Cells within the population are characterised by their age (i.e. time elapsed since they were born). The age-dependent (oxygen-regulated) birth rate is given by a stochastic model of oxygen-dependent cell cycle progression. Once the birth rate is determined, we formulate an age-dependent birth-and-death process, which dictates the time evolution of the cell population. The population is under a feedback loop which controls its steady state size (carrying capacity): cells consume oxygen which in turn fuels cell proliferation. We show that our stochastic model of cell cycle progression allows for heterogeneity within the cell population induced by stochastic effects. Such heterogeneous behaviour is reflected in variations in the proliferation rate. Within this set-up, we have established three main results. First, we have shown that the age to the G1/S transition, which essentially determines the birth rate, exhibits a remarkably simple scaling behaviour. Besides the fact that this simple behaviour emerges from a rather complex model, this allows for a huge simplification of our numerical methodology. A further result is the observation that heterogeneous populations undergo an internal process of quasi-neutral competition. Finally, we investigated the effects of cell-cycle-phase dependent therapies (such as radiation therapy) on heterogeneous populations. In particular, we have studied the case in which the population contains a quiescent sub-population. Our mean-field analysis and numerical simulations confirm that, if the survival fraction of the therapy is too high, rescue of the quiescent population occurs. This gives rise to emergence of resistance

  16. Uncertainty quantification of fast sodium current steady-state inactivation for multi-scale models of cardiac electrophysiology.

    PubMed

    Pathmanathan, Pras; Shotwell, Matthew S; Gavaghan, David J; Cordeiro, Jonathan M; Gray, Richard A

    2015-01-01

    Perhaps the most mature area of multi-scale systems biology is the modelling of the heart. Current models are grounded in over fifty years of research in the development of biophysically detailed models of the electrophysiology (EP) of cardiac cells, but one aspect which is inadequately addressed is the incorporation of uncertainty and physiological variability. Uncertainty quantification (UQ) is the identification and characterisation of the uncertainty in model parameters derived from experimental data, and the computation of the resultant uncertainty in model outputs. It is a necessary tool for establishing the credibility of computational models, and will likely be expected of EP models for future safety-critical clinical applications. The focus of this paper is formal UQ of one major sub-component of cardiac EP models, the steady-state inactivation of the fast sodium current, INa. To better capture average behaviour and quantify variability across cells, we have applied for the first time an 'individual-based' statistical methodology to assess voltage clamp data. Advantages of this approach over a more traditional 'population-averaged' approach are highlighted. The method was used to characterise variability amongst cells isolated from canine epi and endocardium, and this variability was then 'propagated forward' through a canine model to determine the resultant uncertainty in model predictions at different scales, such as of upstroke velocity and spiral wave dynamics. Statistically significant differences between epi and endocardial cells (greater half-inactivation and less steep slope of steady state inactivation curve for endo) was observed, and the forward propagation revealed a lack of robustness of the model to underlying variability, but also surprising robustness to variability at the tissue scale. Overall, the methodology can be used to: (i) better analyse voltage clamp data; (ii) characterise underlying population variability; (iii) investigate

  17. Uncertainty quantification of fast sodium current steady-state inactivation for multi-scale models of cardiac electrophysiology

    PubMed Central

    Shotwell, Matthew S.; Gavaghan, David J.; Cordeiro, Jonathan M.; Gray, Richard A.

    2015-01-01

    Perhaps the most mature area of multi-scale systems biology is the modelling of the heart. Current models are grounded in over fifty years of research in the development of biophysically detailed models of the electrophysiology (EP) of cardiac cells, but one aspect which is inadequately addressed is the incorporation of uncertainty and physiological variability. Uncertainty quantification (UQ) is the identification and characterisation of the uncertainty in model parameters derived from experimental data, and the computation of the resultant uncertainty in model outputs. It is a necessary tool for establishing the credibility of computational models, and will likely be expected of EP models for future safety-critical clinical applications. The focus of this paper is formal UQ of one major sub-component of cardiac EP models, the steady-state inactivation of the fast sodium current, INa. To better capture average behaviour and quantify variability across cells, we have applied for the first time an ‘individual-based’ statistical methodology to assess voltage clamp data. Advantages of this approach over a more traditional ‘population-averaged’ approach are highlighted. The method was used to characterise variability amongst cells isolated from canine epi and endocardium, and this variability was then ‘propagated forward’ through a canine model to determine the resultant uncertainty in model predictions at different scales, such as of upstroke velocity and spiral wave dynamics. Statistically significant differences between epi and endocardial cells (greater half-inactivation and less steep slope of steady state inactivation curve for endo) was observed, and the forward propagation revealed a lack of robustness of the model to underlying variability, but also surprising robustness to variability at the tissue scale. Overall, the methodology can be used to: (i) better analyse voltage clamp data; (ii) characterise underlying population variability; (iii

  18. Multi-scale textural feature extraction and particle swarm optimization based model selection for false positive reduction in mammography.

    PubMed

    Zyout, Imad; Czajkowska, Joanna; Grzegorzek, Marcin

    2015-12-01

    The high number of false positives and the resulting number of avoidable breast biopsies are the major problems faced by current mammography Computer Aided Detection (CAD) systems. False positive reduction is not only a requirement for mass but also for calcification CAD systems which are currently deployed for clinical use. This paper tackles two problems related to reducing the number of false positives in the detection of all lesions and masses, respectively. Firstly, textural patterns of breast tissue have been analyzed using several multi-scale textural descriptors based on wavelet and gray level co-occurrence matrix. The second problem addressed in this paper is the parameter selection and performance optimization. For this, we adopt a model selection procedure based on Particle Swarm Optimization (PSO) for selecting the most discriminative textural features and for strengthening the generalization capacity of the supervised learning stage based on a Support Vector Machine (SVM) classifier. For evaluating the proposed methods, two sets of suspicious mammogram regions have been used. The first one, obtained from Digital Database for Screening Mammography (DDSM), contains 1494 regions (1000 normal and 494 abnormal samples). The second set of suspicious regions was obtained from database of Mammographic Image Analysis Society (mini-MIAS) and contains 315 (207 normal and 108 abnormal) samples. Results from both datasets demonstrate the efficiency of using PSO based model selection for optimizing both classifier hyper-parameters and parameters, respectively. Furthermore, the obtained results indicate the promising performance of the proposed textural features and more specifically, those based on co-occurrence matrix of wavelet image representation technique.

  19. Development of a Blast Event Simulation Process for Multi-Scale Modeling of Composite Armor for Light Weight Vehicles (PREPRINT)

    DTIC Science & Technology

    2011-03-15

    the constitutive micro-level like fiber failures, matrix damage , inelasticity, interfacial debonding to the global structural response level. The MAC...micromechanical analysis establishes the overall elastoplastic behavior of the multiphase inelastic composite. This is expressed as an effective elastic-plastic...fiber failures, matrix damage , interfacial debonding, throughout the structural response. This fully coupled multi-scale simulation frame will be

  20. Resolving the Multi-scale Behavior of Geochemical Weathering in the Critical Zone Using High Resolution Hydro-geochemical Models

    NASA Astrophysics Data System (ADS)

    Pandey, S.; Rajaram, H.

    2015-12-01

    This work investigates hydrologic and geochemical interactions in the Critical Zone (CZ) using high-resolution reactive transport modeling. Reactive transport models can be used to predict the response of geochemical weathering and solute fluxes in the CZ to changes in a dynamic environment, such as those pertaining to human activities and climate change in recent years. The scales of hydrology and geochemistry in the CZ range from days to eons in time and centimeters to kilometers in space. Here, we present results of a multi-dimensional, multi-scale hydro-geochemical model to investigate the role of subsurface heterogeneity on the formation of mineral weathering fronts in the CZ, which requires consideration of many of these spatio-temporal scales. The model is implemented using the reactive transport code PFLOTRAN, an open source subsurface flow and reactive transport code that utilizes parallelization over multiple processing nodes and provides a strong framework for simulating weathering in the CZ. The model is set up to simulate weathering dynamics in the mountainous catchments representative of the Colorado Front Range. Model parameters were constrained based on hydrologic, geochemical, and geophysical observations from the Boulder Creek Critical Zone Observatory (BcCZO). Simulations were performed in fractured rock systems and compared with systems of heterogeneous and homogeneous permeability fields. Tracer simulations revealed that the mean residence time of solutes was drastically accelerated as fracture density increased. In simulations that include mineral reactions, distinct signatures of transport limitations on weathering arose when discrete flow paths were included. This transport limitation was related to both advective and diffusive processes in the highly heterogeneous systems (i.e. fractured media and correlated random permeability fields with σlnk > 3). The well-known time-dependence of mineral weathering rates was found to be the most

  1. Damage and failure modelling of hybrid three-dimensional textile composites: a mesh objective multi-scale approach.

    PubMed

    Patel, Deepak K; Waas, Anthony M

    2016-07-13

    -induced geometric imperfections are included in the simulation, where the FE mesh of the unit cell is generated directly from micro-computed tomography (MCT) real data using a code Simpleware Results from multi-scale analysis for both an idealized perfect geometry and one that includes geometric imperfections are compared with experimental results (Pankow et al. 2012 53rd AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference, Honolulu, HI, 23-26 April 2012 AIAA 2012-1572). This article is part of the themed issue 'Multiscale modelling of the structural integrity of composite materials'.

  2. Multi-scale 3D X-ray Imaging Capabilities at the Advanced Photon Source - Current status and future direction (Invited)

    NASA Astrophysics Data System (ADS)

    DeCarlo, F.; Xiao, X.; Khan, F.; Glowacki, A.; Schwarz, N.; Jacobsen, C.

    2013-12-01

    In x-ray computed μ-tomography (μ-XCT), a thin scintillator screen is coupled to a visible light lens and camera system to obtain micrometer-scale transmission imaging of specimens as large as a few millimeters. Recent advances in detector technology allow collecting these images at unprecedented frame rates. For a high x-ray flux density synchrotron facility like the Advanced Photon Source (APS), the detector exposure time ranges from hundreds of milliseconds to hundreds of picoseconds, making possible to acquire a full 3D micrometer-resolution dataset in less than one second. The micron resolution limitation of parallel x-ray beam projection systems can be overcame by Transmission X-ray Microscopes (TXM) where part of the image magnification is done in x-ray regime using x-ray optics like capillary condensers and Fresnel zone plates. These systems, when installed on a synchrotron x-ray source, can generate 2D images with up to 20 nm resolution with second exposure time and collect a full 3D nano-resolution dataset in few minutes. μ-XCT and TXM systems available at the x-ray imaging beamlines of the APS are routinely used in material science and geoscience applications where high-resolution and fast 3D imaging are instrumental in extracting in situ four-dimensional dynamic information. In this presentation we describe the computational challenges associated with μ-XCT and TXM systems and present the framework and infrastructure developed at the APS to allow for routine multi-scale data integration between the two systems.

  3. Multi-scale 3D X-ray Imaging Capabilities at the Advanced Photon Source - Current status and future direction (Invited)

    NASA Astrophysics Data System (ADS)

    DeCarlo, F.; Xiao, X.; Khan, F.; Glowacki, A.; Schwarz, N.; Jacobsen, C.

    2011-12-01

    In x-ray computed μ-tomography (μ-XCT), a thin scintillator screen is coupled to a visible light lens and camera system to obtain micrometer-scale transmission imaging of specimens as large as a few millimeters. Recent advances in detector technology allow collecting these images at unprecedented frame rates. For a high x-ray flux density synchrotron facility like the Advanced Photon Source (APS), the detector exposure time ranges from hundreds of milliseconds to hundreds of picoseconds, making possible to acquire a full 3D micrometer-resolution dataset in less than one second. The micron resolution limitation of parallel x-ray beam projection systems can be overcame by Transmission X-ray Microscopes (TXM) where part of the image magnification is done in x-ray regime using x-ray optics like capillary condensers and Fresnel zone plates. These systems, when installed on a synchrotron x-ray source, can generate 2D images with up to 20 nm resolution with second exposure time and collect a full 3D nano-resolution dataset in few minutes. μ-XCT and TXM systems available at the x-ray imaging beamlines of the APS are routinely used in material science and geoscience applications where high-resolution and fast 3D imaging are instrumental in extracting in situ four-dimensional dynamic information. In this presentation we describe the computational challenges associated with μ-XCT and TXM systems and present the framework and infrastructure developed at the APS to allow for routine multi-scale data integration between the two systems.

  4. Toward Improving Predictability of Extreme Hydrometeorological Events: the Use of Multi-scale Climate Modeling in the Northern High Plains

    NASA Astrophysics Data System (ADS)

    Munoz-Arriola, F.; Torres-Alavez, J.; Mohamad Abadi, A.; Walko, R. L.

    2014-12-01

    Our goal is to investigate possible sources of predictability of hydrometeorological extreme events in the Northern High Plains. Hydrometeorological extreme events are considered the most costly natural phenomena. Water deficits and surpluses highlight how the water-climate interdependence becomes crucial in areas where single activities drive economies such as Agriculture in the NHP. Nonetheless we recognize the Water-Climate interdependence and the regulatory role that human activities play, we still grapple to identify what sources of predictability could be added to flood and drought forecasts. To identify the benefit of multi-scale climate modeling and the role of initial conditions on flood and drought predictability on the NHP, we use the Ocean Land Atmospheric Model (OLAM). OLAM is characterized by a dynamic core with a global geodesic grid with hexagonal (and variably refined) mesh cells and a finite volume discretization of the full compressible Navier Stokes equations, a cut-grid cell method for topography (that reduces error in computational gradient computation and anomalous vertical dispersion). Our hypothesis is that wet conditions will drive OLAM's simulations of precipitation to wetter conditions affecting both flood forecast and drought forecast. To test this hypothesis we simulate precipitation during identified historical flood events followed by drought events in the NHP (i.e. 2011-2012 years). We initialized OLAM with CFS-data 1-10 days previous to a flooding event (as initial conditions) to explore (1) short-term and high-resolution and (2) long-term and coarse-resolution simulations of flood and drought events, respectively. While floods are assessed during a maximum of 15-days refined-mesh simulations, drought is evaluated during the following 15 months. Simulated precipitation will be compared with the Sub-continental Observation Dataset, a gridded 1/16th degree resolution data obtained from climatological stations in Canada, US, and

  5. Quantifying restoration effectiveness using multi-scale habitat models: implications for sage-grouse in the Great Basin

    USGS Publications Warehouse

    Arkle, Robert S.; Pilliod, David S.; Hanser, Steven E.; Brooks, Matthew L.; Chambers, Jeanne C.; Grace, James B.; Knutson, Kevin C.; Pyke, David A.; Welty, Justin L.

    2014-01-01

    A recurrent challenge in the conservation of wide-ranging, imperiled species is understanding which habitats to protect and whether we are capable of restoring degraded landscapes. For Greater Sage-grouse (Centrocercus urophasianus), a species of conservation concern in the western United States, we approached this problem by developing multi-scale empirical models of occupancy in 211 randomly located plots within a 40 million ha portion of the species' range. We then used these models to predict sage-grouse habitat quality at 826 plots associated with 101 post-wildfire seeding projects implemented from 1990 to 2003. We also compared conditions at restoration sites to published habitat guidelines. Sage-grouse occupancy was positively related to plot- and landscape-level dwarf sagebrush (Artemisia arbuscula, A. nova, A. tripartita) and big sagebrush steppe prevalence, and negatively associated with non-native plants and human development. The predicted probability of sage-grouse occupancy at treated plots was low on average (0.09) and not substantially different from burned areas that had not been treated. Restoration sites with quality habitat tended to occur at higher elevation locations with low annual temperatures, high spring precipitation, and high plant diversity. Of 313 plots seeded after fire, none met all sagebrush guidelines for breeding habitats, but approximately 50% met understory guidelines, particularly for perennial grasses. This pattern was similar for summer habitat. Less than 2% of treated plots met winter habitat guidelines. Restoration actions did not increase the probability of burned areas meeting most guideline criteria. The probability of meeting guidelines was influenced by a latitudinal gradient, climate, and topography. Our results suggest that sage-grouse are relatively unlikely to use many burned areas within 20 years of fire, regardless of treatment. Understory habitat conditions are more likely to be adequate than overstory

  6. Viscoelastic Model for Lung Parenchyma for Multi-Scale Modeling of Respiratory System, Phase II: Dodecahedral Micro-Model

    SciTech Connect

    Freed, Alan D.; Einstein, Daniel R.; Carson, James P.; Jacob, Rick E.

    2012-03-01

    In the first year of this contractual effort a hypo-elastic constitutive model was developed and shown to have great potential in modeling the elastic response of parenchyma. This model resides at the macroscopic level of the continuum. In this, the second year of our support, an isotropic dodecahedron is employed as an alveolar model. This is a microscopic model for parenchyma. A hopeful outcome is that the linkage between these two scales of modeling will be a source of insight and inspiration that will aid us in the final year's activity: creating a viscoelastic model for parenchyma.

  7. MATCH-SALSA - Multi-scale Atmospheric Transport and CHemistry model coupled to the SALSA aerosol microphysics model - Part 1: Model description and evaluation

    NASA Astrophysics Data System (ADS)

    Andersson, C.; Bergström, R.; Bennet, C.; Robertson, L.; Thomas, M.; Korhonen, H.; Lehtinen, K. E. J.; Kokkola, H.

    2014-05-01

    We have implemented the sectional aerosol dynamics model SALSA in the European scale chemistry-transport model MATCH (Multi-scale Atmospheric Transport and Chemistry). The new model is called MATCH-SALSA. It includes aerosol microphysics, with several formulations for nucleation, wet scavenging and condensation. The model reproduces observed higher particle number concentration (PNC) in central Europe and lower concentrations in remote regions. The model PNC size distribution peak occurs at the same or smaller particle size as the observed peak at five measurement sites spread across Europe. Total PNC is underestimated at Northern and Central European sites and accumulation mode PNC is underestimated at all investigated sites. On the other hand the model performs well for particle mass, including secondary inorganic aerosol components. Elemental and organic carbon concentrations are underestimated at many of the sites. Further development is needed, primarily for treatment of secondary organic aerosol, both in terms of biogenic emissions and chemical transformation, and for nitrogen gas-particle partitioning. Updating the biogenic SOA scheme will likely have a large impact on modeled PM2.5 and also affect the model performance for PNC through impacts on nucleation and condensation. An improved nitrogen partitioning model may also improve the description of condensational growth.

  8. MATCH-SALSA - Multi-scale Atmospheric Transport and CHemistry model coupled to the SALSA aerosol microphysics model - Part 1: Model description and evaluation

    NASA Astrophysics Data System (ADS)

    Andersson, C.; Bergström, R.; Bennet, C.; Robertson, L.; Thomas, M.; Korhonen, H.; Lehtinen, K. E. J.; Kokkola, H.

    2015-02-01

    We have implemented the sectional aerosol dynamics model SALSA (Sectional Aerosol module for Large Scale Applications) in the European-scale chemistry-transport model MATCH (Multi-scale Atmospheric Transport and Chemistry). The new model is called MATCH-SALSA. It includes aerosol microphysics, with several formulations for nucleation, wet scavenging and condensation. The model reproduces observed higher particle number concentration (PNC) in central Europe and lower concentrations in remote regions. The modeled PNC size distribution peak occurs at the same or smaller particle size as the observed peak at four measurement sites spread across Europe. Total PNC is underestimated at northern and central European sites and accumulation-mode PNC is underestimated at all investigated sites. The low nucleation rate coefficient used in this study is an important reason for the underestimation. On the other hand, the model performs well for particle mass (including secondary inorganic aerosol components), while elemental and organic carbon concentrations are underestimated at many of the sites. Further development is needed, primarily for treatment of secondary organic aerosol, in terms of biogenic emissions and chemical transformation. Updating the biogenic secondary organic aerosol (SOA) scheme will likely have a large impact on modeled PM2.5 and also affect the model performance for PNC through impacts on nucleation and condensation.

  9. Building and Refining Protein Models within Cryo-electron Microscopy Density Maps Based on Homology Modeling and Multi-scale Structure Refinement

    PubMed Central

    Zhu, Jiang; Cheng, Lingpeng; Fang, Qin; Hong Zhou, Z.; Honig, Barry

    2010-01-01

    Summary Automatic modeling methods using cryo-electron microscopy (cryoEM) density maps as constrains are promising approaches to building atomic models of individual proteins or protein domains. However, their application to large macromolecular assemblies has not been possible largely due to computational limitations inherent to such unsupervised methods. Here we describe a new method, EM-IMO, for building, modifying and refining local structures of protein models using cryoEM maps as a constraint. As a supervised refinement method, EM-IMO allows users to specify parameters derived from inspections, so as to guide, and as a consequence, significantly speed up the refinement. An EM-IMO-based refinement protocol is first benchmarked on a data set of 50 homology models using simulated density maps. A multi-scale refinement strategy that combines EM-IMO-based and molecular dynamics (MD)-based refinement is then applied to build backbone models for the seven conformers of the five capsid proteins in our near-atomic resolution cryoEM map of the grass carp reovirus (GCRV) virion, a member of the aquareovirus genus of the Reoviridae family. The refined models allow us to reconstruct a backbone model of the entire GCRV capsid and provide valuable functional insights that are described in the accompanying publication. Our study demonstrates that the integrated use of homology modeling and a multi-scale refinement protocol that combines supervised and automated structure refinement offers a practical strategy for building atomic models based on medium- to high-resolution cryoEM density maps. PMID:20109465

  10. Multi-scale Measurements and Modeling to Verify and Attribute Carbon Dioxide Emissions from Four Corners Power Plants

    NASA Astrophysics Data System (ADS)

    Dubey, M. K.; Love, S. P.; Henderson, B. G.; Lee, S.; Costigan, K. R.; Reisner, J.; Flowers, B. A.; Chylek, P.

    2011-12-01

    inventories like Vulcan. WRF-Chem employs multiple nested grids and high resolution topography to simulate atmospheric variability ranging from synoptic scales to micro-scales (~200 m), while including locally developed flows influenced by the nearby complex terrain of the San Juan Mountains. The simulated local atmospheric dynamics are provided to force the HIGRAD plume model, which links meso-scale atmospheric variability to the small-scale simulation of the power plant plumes (~10m). Our multi-scale forward modeling simulations are compared with our column and in situ observations of CO2, other greenhouse gases and pollutants for specific days. We use this to quantify the current ability of remote and in situ sensing measurements to quantify emissions in a relatively simple environment. Finally, we examine satellite data (CO2 and CH4 from GOSAT and NO2 from OMI) for signals over Four Corners and assess the value added for longer-term trend analysis. We gratefully acknowledge members of the TCCON (D. Wunch and P. Wennberg) and HIPPO (S. Wofsy and B. Stephens) teams for their input and guidance.

  11. Quantifying rock's structural fabric: a multi-scale hierarchical approach to natural fracture systems and stochastic modelling

    NASA Astrophysics Data System (ADS)

    Hardebol, Nico; Bertotti, Giovanni; Weltje, Gert Jan

    2014-05-01

    We propose the description of fracture-fault systems in terms of a multi-scale hierarchical network. In most generic form, such arrangement is referred to as a structural fabric and applicable across the length scale spectrum. The statistical characterisation combines the fracture length and orientation distributions and intersection-termination relationships. The aim is a parameterised description of the network that serves as input in stochastic network simulations that should reproduce the essence of natural fracture networks and encompass its variability. The quality of the stochastically generated fabric is determined by comparison with deterministic descriptions on which the model parameterisation is based. Both the deterministic and stochastic derived fracture network description can serve as input in fluid flow or mechanical simulations that accounts explicitly for the discrete features and the response of the system can be compared. The deterministic description of our current study in the framework of tight gas reservoirs is obtained from coastal pavements that expose a horizontal slice through a fracture-fault network system in fine grained sediments in Yorkshire, UK. Fracture hierarchies have often been described at one observation scale as a two-tier hierarchy in terms of 1st order systematic joints and 2nd order cross-joints. New in our description is the bridging between km-sized faults with notable displacement down to sub-meter scale shear and opening mode fractures. This study utilized a drone to obtain cm-resolution imagery of pavements from ~30m altitude and the large coverage up to 1-km by flying at a ~80m. This unique set of images forms the basis for the digitizing of the fracture-fault pattern and helped determining the nested nature of the network as well as intersection and abutment relationships. Fracture sets were defined from the highest to lowest hierarchical order and probability density functions were defined for the length

  12. A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation.

    PubMed

    Xiao, Li; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray

    2014-11-25

    A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design.

  13. A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation

    PubMed Central

    Xiao, Li; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray

    2014-01-01

    A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design. PMID:25404761

  14. Corrosion chemistry closing comments: opportunities in corrosion science facilitated by operando experimental characterization combined with multi-scale computational modelling.

    PubMed

    Scully, John R

    2015-01-01

    Recent advances in characterization tools, computational capabilities, and theories have created opportunities for advancement in understanding of solid-fluid interfaces at the nanoscale in corroding metallic systems. The Faraday Discussion on Corrosion Chemistry in 2015 highlighted some of the current needs, gaps and opportunities in corrosion science. Themes were organized into several hierarchical categories that provide an organizational framework for corrosion. Opportunities to develop fundamental physical and chemical data which will enable further progress in thermodynamic and kinetic modelling of corrosion were discussed. These will enable new and better understanding of unit processes that govern corrosion at the nanoscale. Additional topics discussed included scales, films and oxides, fluid-surface and molecular-surface interactions, selected topics in corrosion science and engineering as well as corrosion control. Corrosion science and engineering topics included complex alloy dissolution, local corrosion, and modelling of specific corrosion processes that are made up of collections of temporally and spatially varying unit processes such as oxidation, ion transport, and competitive adsorption. Corrosion control and mitigation topics covered some new insights on coatings and inhibitors. Further advances in operando or in situ experimental characterization strategies at the nanoscale combined with computational modelling will enhance progress in the field, especially if coupling across length and time scales can be achieved incorporating the various phenomena encountered in corrosion. Readers are encouraged to not only to use this ad hoc organizational scheme to guide their immersion into the current opportunities in corrosion chemistry, but also to find value in the information presented in their own ways.

  15. A Semi-Empirical Multi-Scale Dynamic Monte Carlo Model of Organic Photovoltaic Performance in RIR-MAPLE Bulk Heterojunction Films

    NASA Astrophysics Data System (ADS)

    Stiff-Roberts, Adrienne; Atewologun, Ayomide

    A semi-empirical method for investigating the performance of OPVs in resonant infrared, matrix-assisted pulsed laser evaporation (RIR-MAPLE) films is explored. Emulsion-based RIR-MAPLE offers a unique experimental backdrop for investigating trends through simulation and gaining a better understanding of how different thin film characteristics impact OPV device performance. A novel multi-scale formulation of the Dynamic Monte Carlo (DMC) model is developed based on observable morphology features. Specifically, using confocal microscopy, we observe the presence of micro-scale regimes of pure materials and nano-scale regions of the composite blend. This enables us to assign weighted percentages to DMC implementations on two different scales: the microscale and nanoscale regions. In addition to this, we use input simulation parameters acquired by characterization of as-deposited films. The semi-empirical multi-scale model presented serves as a unique simulation opportunity for exploring different properties of RIR-MAPLE deposited OPVs, their effects on OPV performance and potential design routes for improving device efficiencies. This work was supported, in part, by the Office of Naval Research under Grant N00014-10-1-0481 and the NSF Triangle MRSEC on Soft Matter.

  16. A multi-scale cardiovascular system model can account for the load-dependence of the end-systolic pressure-volume relationship

    PubMed Central

    2013-01-01

    Background The end-systolic pressure-volume relationship is often considered as a load-independent property of the heart and, for this reason, is widely used as an index of ventricular contractility. However, many criticisms have been expressed against this index and the underlying time-varying elastance theory: first, it does not consider the phenomena underlying contraction and second, the end-systolic pressure volume relationship has been experimentally shown to be load-dependent. Methods In place of the time-varying elastance theory, a microscopic model of sarcomere contraction is used to infer the pressure generated by the contraction of the left ventricle, considered as a spherical assembling of sarcomere units. The left ventricle model is inserted into a closed-loop model of the cardiovascular system. Finally, parameters of the modified cardiovascular system model are identified to reproduce the hemodynamics of a normal dog. Results Experiments that have proven the limitations of the time-varying elastance theory are reproduced with our model: (1) preload reductions, (2) afterload increases, (3) the same experiments with increased ventricular contractility, (4) isovolumic contractions and (5) flow-clamps. All experiments simulated with the model generate different end-systolic pressure-volume relationships, showing that this relationship is actually load-dependent. Furthermore, we show that the results of our simulations are in good agreement with experiments. Conclusions We implemented a multi-scale model of the cardiovascular system, in which ventricular contraction is described by a detailed sarcomere model. Using this model, we successfully reproduced a number of experiments that have shown the failing points of the time-varying elastance theory. In particular, the developed multi-scale model of the cardiovascular system can capture the load-dependence of the end-systolic pressure-volume relationship. PMID:23363818

  17. On the impact of modelling assumptions in multi-scale, subject-specific models of aortic haemodynamics.

    PubMed

    Alastruey, Jordi; Xiao, Nan; Fok, Henry; Schaeffter, Tobias; Figueroa, C Alberto

    2016-06-01

    Simulation of haemodynamics has become increasingly popular within the research community. Irrespective of the modelling approach (zero-dimensional (0D), one-dimensional (1D) or three-dimensional (3D)), in vivo measurements are required to personalize the arterial geometry, material properties and boundary conditions of the computational model. Limitations in in vivo data acquisition often result in insufficient information to determine all model parameters and, hence, arbitrary modelling assumptions. Our goal was to minimize and understand the impact of modelling assumptions on the simulated blood pressure, flow and luminal area waveforms by studying a small region of the systemic vasculature-the upper aorta-and acquiring a rich array of non-invasive magnetic resonance imaging and tonometry data from a young healthy volunteer. We first investigated the effect of different modelling assumptions for boundary conditions and material parameters in a 1D/0D simulation framework. Strategies were implemented to mitigate the impact of inconsistencies in the in vivo data. Average relative errors smaller than 7% were achieved between simulated and in vivo waveforms. Similar results were obtained in a 3D/0D simulation framework using the same inflow and outflow boundary conditions and consistent geometrical and mechanical properties. We demonstrated that accurate subject-specific 1D/0D and 3D/0D models of aortic haemodynamics can be obtained using non-invasive clinical data while minimizing the number of arbitrary modelling decisions.

  18. Permeability of fiber reinforcements for liquid composite molding: Sequential multi-scale investigations into numerical flow modeling on the micro- and meso-scale

    NASA Astrophysics Data System (ADS)

    Luchini, Timothy John Franklin

    Composites are complex material mixtures, known to have high amounts of variability, with unique properties at the micro-, meso-, and macro-scales. In the context of advanced textile composite reinforcements, micro-scale refers to aligned fibers and toughening agents in a disordered arrangement; meso-scale is the woven, braided, or stitched fabric geometry (which compacts to various volume fractions); and macro-scale is the component or sub-component being produced for a mechanical application. The Darcy-based permeability is an important parameter for modeling and understanding the flow profile and fill times for liquid composite molding. Permeability of composite materials can vary widely from the micro- to macro-scales. For example, geometric factors like compaction and ply layup affect the component permeability at the meso- and macro-scales. On the micro-scale the permeability will be affected by the packing arrangement of the fibers and fiber volume fraction. On any scale, simplifications to the geometry can be made to treat the fiber reinforcement as a porous media. Permeability has been widely studied in both experimental and analytical frameworks, but less attention has focused on the ability of numerical tools to predict the permeability of reinforced composite materials. This work aims at (1) predicting permeability at various scales of interest and (2) developing a sequential, multi-scale, numerical modeling approach on the micro- and meso-scales. First, a micro-scale modeling approach is developed, including a geometry generation tool and a fluids-based numerical permeability solver. This micro-scale model included all physical fibers and derived the empirical permeability constant directly though numerical simulation. This numerical approach was compared with literature results for perfect packing arrangements, and the results were shown to be comparable with previous work. The numerical simulations described here also extended these previous

  19. The air quality forecast in Beijing with Community Multi-scale Air Quality Modeling (CMAQ) System: model evaluation and improvement

    NASA Astrophysics Data System (ADS)

    Wu, Q.

    2013-12-01

    The MM5-SMOKE-CMAQ model system, which is developed by the United States Environmental Protection Agency(U.S. EPA) as the Models-3 system, has been used for the daily air quality forecast in the Beijing Municipal Environmental Monitoring Center(Beijing MEMC), as a part of the Ensemble Air Quality Forecast System for Beijing(EMS-Beijing) since the Olympic Games year 2008. In this study, we collect the daily forecast results of the CMAQ model in the whole year 2010 for the model evaluation. The results show that the model play a good model performance in most days but underestimate obviously in some air pollution episode. A typical air pollution episode from 11st - 20th January 2010 was chosen, which the air pollution index(API) of particulate matter (PM10) observed by Beijing MEMC reaches to 180 while the prediction of PM10-API is about 100. Taking in account all stations in Beijing, including urban and suburban stations, three numerical methods are used for model improvement: firstly, enhance the inner domain with 4km grids, the coverage from only Beijing to the area including its surrounding cities; secondly, update the Beijing stationary area emission inventory, from statistical county-level to village-town level, that would provide more detail spatial informance for area emissions; thirdly, add some industrial points emission in Beijing's surrounding cities, the latter two are both the improvement of emission. As the result, the peak of the nine national standard stations averaged PM10-API, which is simulated by CMAQ as daily hindcast PM10-API, reach to 160 and much near to the observation. The new results show better model performance, which the correlation coefficent is 0.93 in national standard stations average and 0.84 in all stations, the relative error is 15.7% in national standard stations averaged and 27% in all stations. The time series of 9 national standard in Beijing urban The scatter diagram of all stations in Beijing, the red is the forecast and

  20. Multi-Scale Modelling of Deformation and Fracture in a Biomimetic Apatite-Protein Composite: Molecular-Scale Processes Lead to Resilience at the μm-Scale

    PubMed Central

    Zahn, Dirk; Duchstein, Patrick

    2016-01-01

    Fracture mechanisms of an enamel-like hydroxyapatite-collagen composite model are elaborated by means of molecular and coarse-grained dynamics simulation. Using fully atomistic models, we uncover molecular-scale plastic deformation and fracture processes initiated at the organic-inorganic interface. Furthermore, coarse-grained models are developed to investigate fracture patterns at the μm-scale. At the meso-scale, micro-fractures are shown to reduce local stress and thus prevent material failure after loading beyond the elastic limit. On the basis of our multi-scale simulation approach, we provide a molecular scale rationalization of this phenomenon, which seems key to the resilience of hierarchical biominerals, including teeth and bone. PMID:27300748

  1. Image-based multi-scale modelling and validation of radio-frequency ablation in liver tumours.

    PubMed

    Payne, Stephen; Flanagan, Ronan; Pollari, Mika; Alhonnoro, Tuomas; Bost, Claire; O'Neill, David; Peng, Tingying; Stiegler, Philipp

    2011-11-13

    The treatment of cancerous tumours in the liver remains clinically challenging, despite the wide range of treatment possibilities, including radio-frequency ablation (RFA), high-intensity focused ultrasound and resection, which are currently available. Each has its own advantages and disadvantages. For non- or minimally invasive modalities, such as RFA, considered here, it is difficult to monitor the treatment in vivo. This is particularly problematic in the liver, where large blood vessels act as heat sinks, dissipating delivered heat and shrinking the size of the lesion (the volume damaged by the heat treatment) locally; considerable experience is needed on the part of the clinician to optimize the heat treatment to prevent recurrence. In this paper, we outline our work towards developing a simulation tool kit that could be used both to optimize treatment protocols in advance and to train the less-experienced clinicians for RFA treatment of liver tumours. This tool is based on a comprehensive mathematical model of bio-heat transfer and cell death. We show how simulations of ablations in two pigs, based on individualized imaging data, compare directly with experimentally measured lesion sizes and discuss the likely sources of error and routes towards clinical implementation. This is the first time that such a 'loop' of mathematical modelling and experimental validation in vivo has been performed in this context, and such validation enables us to make quantitative estimates of error.

  2. Impact of air traffic emissions on airport air quality. Multi-scale modeling, test bed and field measurements

    NASA Astrophysics Data System (ADS)

    Ramaroson, R.; Vuillot, F.; Durand, Y.; Courbet, B.; Janin, F.; Copalle, A.; Guin, C.; Paux, E.; Vannier, F.; Talbaut, M.; Weill, M.

    2004-12-01

    Air traffic emissions are playing a significant role in airport air quality. Engine emissions contribute to the ozone and PM formation. There is an emergence of a need to develop advanced numerical tools and airport emission databases for air pollution studies. Field monitoring at airports necessary to support model assessment is still limited in time and space. The French ONERA AIRPUR project has focused on three objectives: emission inventories; dispersion models; field measurements. Results are presented and discussed in this paper. The ground spatial distribution of LTO emissions using realistic aircraft trajectories, aircraft-engine classification by ICAO, fuel flow methodology and diurnal variations of fleet number, is presented and discussed. Exhaust species time evolution is simulated using a chemical-dispersion model. Results show high emissions of NOx during LTO, and a maximum of CO and Hydrocarbons during taxi. Depending on seasons, the NOx lifetime is varying differently; lower concentration is calculated far away from LTO emissions. Longer-lived pollutants such as ozone are formed downstream and require the use of advanced dispersion models. For this reason, two interactive models coupling the micro and the regional scales are developed and used in this work. A 3D CFD model (CEDRE) simulates the flow characteristics around buildings and the dispersion of emissions. CEDRE boundary conditions are provided by the 3D nested dispersion model MEDIUM/MM5, which includes a surface boundary layer chemistry and calculates the concentration of pollutants from the local to the airport vicinities. The CFD results show a tracer accumulation calculated downstream beside terminals, consistent with observations at some mega-airports. Sensibility studies are conducted to highlight the impact of emissions on ozone formation with MEDIUM. Results show that longer-lived species are produced downstream, their concentration depending on NOx, aromatics and VOC released by

  3. Targeting the biophysical properties of the myeloma initiating cell niches: a pharmaceutical synergism analysis using multi-scale agent-based modeling.

    PubMed

    Su, Jing; Zhang, Le; Zhang, Wen; Choi, Dong Song; Wen, Jianguo; Jiang, Beini; Chang, Chung-Che; Zhou, Xiaobo

    2014-01-01

    Multiple myeloma, the second most common hematological cancer, is currently incurable due to refractory disease relapse and development of multiple drug resistance. We and others recently established the biophysical model that myeloma initiating (stem) cells (MICs) trigger the stiffening of their niches via SDF-1/CXCR4 paracrine; The stiffened niches then promote the colonogenesis of MICs and protect them from drug treatment. In this work we examined in silico the pharmaceutical potential of targeting MIC niche stiffness to facilitate cytotoxic chemotherapies. We first established a multi-scale agent-based model using the Markov Chain Monte Carlo approach to recapitulate the niche stiffness centric, pro-oncogenetic positive feedback loop between MICs and myeloma-associated bone marrow stromal cells (MBMSCs), and investigated the effects of such intercellular chemo-physical communications on myeloma development. Then we used AMD3100 (to interrupt the interactions between MICs and their stroma) and Bortezomib (a recently developed novel therapeutic agent) as representative drugs to examine if the biophysical properties of myeloma niches are drugable. Results showed that our model recaptured the key experimental observation that the MBMSCs were more sensitive to SDF-1 secreted by MICs, and provided stiffer niches for these initiating cells and promoted their proliferation and drug resistance. Drug synergism analysis suggested that AMD3100 treatment undermined the capability of MICs to modulate the bone marrow microenvironment, and thus re-sensitized myeloma to Bortezomib treatments. This work is also the first attempt to virtually visualize in 3D the dynamics of the bone marrow stiffness during myeloma development. In summary, we established a multi-scale model to facilitate the translation of the niche-stiffness centric myeloma model as well as experimental observations to possible clinical applications. We concluded that targeting the biophysical properties of stem

  4. Development of Multi-Scale Modeling Software for Entangled Soft Matter in Advanced Soldier Protection

    DTIC Science & Technology

    2011-12-06

    1) where J = (1 + 1/ß) K is the normalization constant , 6(i,j) is the Kronecker delta func- tion, /VK.-V is the total number of Kuhn steps in a...times, k& is the Boltzmann constant , and ß is a parameter that depends on entanglement density and approximately equal to iVe — 1 for long chains...Brownian forces as well as free energy differences, TK is a time constant related to the friction coefficient of a single step in the chain, which

  5. Complex three dimensional modelling of porous media using high performance computing and multi-scale incompressible approach

    NASA Astrophysics Data System (ADS)

    Martin, R.; Orgogozo, L.; Noiriel, C. N.; Guibert, R.; Golfier, F.; Debenest, G.; Quintard, M.

    2013-05-01

    computed by sending batteries of codes in a mass production procedure. Some constraints can now be provided for poro-elastic imaging at the scale of reservoirs, for CO2 storage monitoring or geophysical exploration. 1. Golfier F. et al., Biofilms in porous media: Development of macroscopic transport equations va volume averaging with closure for local mass equilibrium conditions, Advances in Water Resources, 32, 463-485 (2009). 2. Orgogozo L. et al., Upscaling of transport processes in porous media with biofilms in non-equilibrium conditions, Advances in Water Resources, 33(5), 585-600 (2010). 3. Davit Y. et al., Modeling non-equilibrium mass transport in biologically reactive porous media, Advances in Water Resources, 33, 1075-1093, (2010). 4. Davit Y. et al., Imaging biofilm in porous media using X-ray computed micro-tomography, Journal of Microscopy, 242(1), 15-25 (2010). 5. Noiriel C. et al., Upscaling calcium carbonate precipitation rates from pore to continuum scale, Chemical Geology, 318-319, 60-74 (2012).

  6. A multi-scale finite element model for investigation of chondrocyte mechanics in normal and medial meniscectomy human knee joint during walking.

    PubMed

    Tanska, Petri; Mononen, Mika E; Korhonen, Rami K

    2015-06-01

    Mechanical signals experienced by chondrocytes (articular cartilage cells) modulate cell synthesis and cartilage health. Multi-scale modeling can be used to study how forces are transferred from joint surfaces through tissues to chondrocytes. Therefore, estimation of chondrocyte behavior during certain physical activities, such as walking, could provide information about how cells respond to normal and abnormal loading in joints. In this study, a 3D multi-scale model was developed for evaluating chondrocyte and surrounding peri- and extracellular matrix responses during gait loading within healthy and medial meniscectomy knee joints. The knee joint geometry was based on MRI, whereas the input used for gait loading was obtained from the literature. Femoral and tibial cartilages were modeled as fibril-reinforced poroviscoelastic materials, whereas menisci were considered as transversely isotropic. Fluid pressures in the chondrocyte and cartilage tissue increased up to 2MPa (an increase of 30%) in the meniscectomy joint compared to the normal, healthy joint. The elevated level of fluid pressure was observed during the entire stance phase of gait. A medial meniscectomy caused substantially larger (up to 60%) changes in maximum principal strains in the chondrocyte compared to those in the peri- or extracellular matrices. Chondrocyte volume or morphology did not change substantially due to a medial meniscectomy. Current findings suggest that during walking chondrocyte deformations are not substantially altered due to a medial meniscectomy, while abnormal joint loading exposes chondrocytes to elevated levels of fluid pressure and maximum principal strains (compared to strains in the peri- or extracellular matrices). These might contribute to cell viability and the onset of osteoarthritis.

  7. Evaluation of the Mesoscale Meteorological Model (MM5)-Community Multi-Scale Air Quality Model (CMAQ) performance in hindcast and forecast of ground-level ozone.

    PubMed

    Nghiem, Le Hoang; Kim Oanh, Nguyen Thi

    2008-10-01

    This paper presents the first attempt to apply the Mesoscale Meteorological Model (MM5)-Community Multi-Scale Air Quality Model (CMAQ) model system to simulate ground-level ozone (O3) over the continental Southeast Asia (CSEA) region for both hindcast and forecast purposes. Hindcast simulation was done over the CSEA domain for two historical O3 episodes, January 26-29, 2004 (January episode, northeast monsoon) and March 24-26, 2004 (March episode, southwest monsoon). Experimental forecast was done for next-day hourly O3 during January 2006 over the central part of Thailand (CENTHAI). Available data from 20 ambient monitoring stations in Thailand and 3 stations in Ho Chi Minh City, Vietnam, were used for the episode analysis and for the model performance evaluation. The year 2000 anthropogenic emission inventory prepared by the Center for Global and Regional Environmental Research at the University of Iowa was projected to the simulation year on the basis of the regional average economic growth rate. Hourly emission in urban areas was prepared using ambient carbon monoxide concentration as a surrogate for the emission intensity. Biogenic emissions were estimated based on data from the Global Emissions Inventory Activity. Hindcast simulations (CSEA) were performed with 0.5 degree x 0.5 degree resolution, whereas forecast simulations (CENTHAI) were done with 0.1 degree x 0.1 degree hourly emission input data. MM5-CMAQ model system performance during the selected episodes satisfactorily met U.S. Environmental Protection Agency criteria for O3 for most simulated days. The experiment forecast for next-day hourly O3 in January 2006 yielded promising results. Modeled plumes of ozone in both hindcast and forecast cases agreed with the main wind fields and extended over considerable downwind distances from large urban areas.

  8. Development of a Patient-Specific Multi-Scale Model to Understand Atherosclerosis and Calcification Locations: Comparison with In vivo Data in an Aortic Dissection

    PubMed Central

    Alimohammadi, Mona; Pichardo-Almarza, Cesar; Agu, Obiekezie; Díaz-Zuccarini, Vanessa

    2016-01-01

    Vascular calcification results in stiffening of the aorta and is associated with hypertension and atherosclerosis. Atherogenesis is a complex, multifactorial, and systemic process; the result of a number of factors, each operating simultaneously at several spatial and temporal scales. The ability to predict sites of atherogenesis would be of great use to clinicians in order to improve diagnostic and treatment planning. In this paper, we present a mathematical model as a tool to understand why atherosclerotic plaque and calcifications occur in specific locations. This model is then used to analyze vascular calcification and atherosclerotic areas in an aortic dissection patient using a mechanistic, multi-scale modeling approach, coupling patient-specific, fluid-structure interaction simulations with a model of endothelial mechanotransduction. A number of hemodynamic factors based on state-of-the-art literature are used as inputs to the endothelial permeability model, in order to investigate plaque and calcification distributions, which are compared with clinical imaging data. A significantly improved correlation between elevated hydraulic conductivity or volume flux and the presence of calcification and plaques was achieved by using a shear index comprising both mean and oscillatory shear components (HOLMES) and a non-Newtonian viscosity model as inputs, as compared to widely used hemodynamic indicators. The proposed approach shows promise as a predictive tool. The improvements obtained using the combined biomechanical/biochemical modeling approach highlight the benefits of mechanistic modeling as a powerful tool to understand complex phenomena and provides insight into the relative importance of key hemodynamic parameters. PMID:27445834

  9. Cell mass and cell cycle dynamics of an asynchronous budding yeast population: experimental observations, flow cytometry data analysis, and multi-scale modeling.

    PubMed

    Lencastre Fernandes, Rita; Carlquist, Magnus; Lundin, Luisa; Heins, Anna-Lena; Dutta, Abhishek; Sørensen, Søren J; Jensen, Anker D; Nopens, Ingmar; Lantz, Anna Eliasson; Gernaey, Krist V

    2013-03-01

    Despite traditionally regarded as identical, cells in a microbial cultivation present a distribution of phenotypic traits, forming a heterogeneous cell population. Moreover, the degree of heterogeneity is notably enhanced by changes in micro-environmental conditions. A major development in experimental single-cell studies has taken place in the last decades. It has however not been fully accompanied by similar contributions within data analysis and mathematical modeling. Indeed, literature reporting, for example, quantitative analyses of experimental single-cell observations and validation of model predictions for cell property distributions against experimental data is scarce. This study focuses on the experimental and mathematical description of the dynamics of cell size and cell cycle position distributions, of a population of Saccharomyces cerevisiae, in response to the substrate consumption observed during batch cultivation. The good agreement between the proposed multi-scale model (a population balance model [PBM] coupled to an unstructured model) and experimental data (both the overall physiology and cell size and cell cycle distributions) indicates that a mechanistic model is a suitable tool for describing the microbial population dynamics in a bioreactor. This study therefore contributes towards the understanding of the development of heterogeneous populations during microbial cultivations. More generally, it consists of a step towards a paradigm change in the study and description of cell cultivations, where average cell behaviors observed experimentally now are interpreted as a potential joint result of various co-existing single-cell behaviors, rather than a unique response common to all cells in the cultivation.

  10. Spatial patterns and eco-epidemiological systems--part I: multi-scale spatial modelling of the occurrence of Chagas disease insect vectors.

    PubMed

    Roux, Emmanuel; de Fátima Venâncio, Annamaria; Girres, Jean-François; Romaña, Christine A

    2011-11-01

    Studies that explicitly and specifically take into account the spatial dimension within the study of eco-epidemiological systems remain rare. Our approach of modelling the spatial and/or temporal properties of the entomological and/or epidemiological data before their mapping with possible explanatory variables, objectively underline the significant patterns at different scales. The domiciliary and peri-domiciliary presence and abundance of juvenile and adult vectors of the Chagas disease (Triatoma sordida and Panstrongylus geniculatus) in Bahia state in northeast Brazil, has been modelled by automatically identifying significant multi-scale spatial patterns of the entomological data by the application and adoption of the spatial modelling methodology proposed by Dray et al. (2006) and based on principal coordinate analysis of neighbour matrices. We found that entomological data can be modelled by a set of eigenvectors that present a significant Moran's I index of spatial autocorrelation. The models for juvenile and adult vectors are defined by 28 and 32 eigenvectors that explain 82.3% and 79.9%, respectively, of the total data variances. The results support insect presence as the outcome both of a local scale "near-to-near" dispersal and an infestation from the wild, surrounding environment that produces a higher insect density at the village periphery.

  11. Cost and time-effective method for multi-scale measures of rugosity, fractal dimension, and vector dispersion from coral reef 3D models.

    PubMed

    Young, G C; Dey, S; Rogers, A D; Exton, D

    2017-01-01

    We present a method to construct and analyse 3D models of underwater scenes using a single cost-effective camera on a standard laptop with (a) free or low-cost software, (b) no computer programming ability, and (c) minimal man hours for both filming and analysis. This study focuses on four key structural complexity metrics: point-to-point distances, linear rugosity (R), fractal dimension (D), and vector dispersion (1/k). We present the first assessment of accuracy and precision of structure-from-motion (SfM) 3D models from an uncalibrated GoPro™ camera at a small scale (4 m2) and show that they can provide meaningful, ecologically relevant results. Models had root mean square errors of 1.48 cm in X-Y and 1.35 in Z, and accuracies of 86.8% (R), 99.6% (D at scales 30-60 cm), 93.6% (D at scales 1-5 cm), and 86.9 (1/k). Values of R were compared to in-situ chain-and-tape measurements, while values of D and 1/k were compared with ground truths from 3D printed objects modelled underwater. All metrics varied less than 3% between independently rendered models. We thereby improve and rigorously validate a tool for ecologists to non-invasively quantify coral reef structural complexity with a variety of multi-scale metrics.

  12. Scale separation for multi-scale modeling of free-surface and two-phase flows with the conservative sharp interface method

    SciTech Connect

    Han, L.H. Hu, X.Y. Adams, N.A.

    2015-01-01

    In this paper we present a scale separation approach for multi-scale modeling of free-surface and two-phase flows with complex interface evolution. By performing a stimulus-response operation on the level-set function representing the interface, separation of resolvable and non-resolvable interface scales is achieved efficiently. Uniform positive and negative shifts of the level-set function are used to determine non-resolvable interface structures. Non-resolved interface structures are separated from the resolved ones and can be treated by a mixing model or a Lagrangian-particle model in order to preserve mass. Resolved interface structures are treated by the conservative sharp-interface model. Since the proposed scale separation approach does not rely on topological information, unlike in previous work, it can be implemented in a straightforward fashion into a given level set based interface model. A number of two- and three-dimensional numerical tests demonstrate that the proposed method is able to cope with complex interface variations accurately and significantly increases robustness against underresolved interface structures.

  13. Multi-Scale Infrastructure Assessment

    EPA Science Inventory

    The U.S. Environmental Protection Agency’s (EPA) multi-scale infrastructure assessment project supports both water resource adaptation to climate change and the rehabilitation of the nation’s aging water infrastructure by providing tools, scientific data and information to progra...

  14. Modeling the Distribution of African Savanna Elephants in Kruger National Park: AN Application of Multi-Scale GLOBELAND30 Data

    NASA Astrophysics Data System (ADS)

    Xu, W.; Hays, B.; Fayrer-Hosken, R.; Presotto, A.

    2016-06-01

    The ability of remote sensing to represent ecologically relevant features at multiple spatial scales makes it a powerful tool for studying wildlife distributions. Species of varying sizes perceive and interact with their environment at differing scales; therefore, it is important to consider the role of spatial resolution of remotely sensed data in the creation of distribution models. The release of the Globeland30 land cover classification in 2014, with its 30 m resolution, presents the opportunity to do precisely that. We created a series of Maximum Entropy distribution models for African savanna elephants (Loxodonta africana) using Globeland30 data analyzed at varying resolutions. We compared these with similarly re-sampled models created from the European Space Agency's Global Land Cover Map (Globcover). These data, in combination with GIS layers of topography and distance to roads, human activity, and water, as well as elephant GPS collar data, were used with MaxEnt software to produce the final distribution models. The AUC (Area Under the Curve) scores indicated that the models created from 600 m data performed better than other spatial resolutions and that the Globeland30 models generally performed better than the Globcover models. Additionally, elevation and distance to rivers seemed to be the most important variables in our models. Our results demonstrate that Globeland30 is a valid alternative to the well-established Globcover for creating wildlife distribution models. It may even be superior for applications which require higher spatial resolution and less nuanced classifications.

  15. Clouds, weather, climate, and modeling for K-12 and public audiences from the Center for Multi-scale Modeling of Atmospheric Processes

    NASA Astrophysics Data System (ADS)

    Foster, S. Q.; Johnson, R. M.; Randall, D. A.; Denning, A.; Russell, R. M.; Gardiner, L. S.; Hatheway, B.; Jones, B.; Burt, M. A.; Genyuk, J.

    2010-12-01

    The need for improving the representation of cloud processes in climate models has been one of the most important limitations of the reliability of climate-change simulations. Now in its fifth year, the National Science Foundation-funded Center for Multi-scale Modeling of Atmospheric Processes (CMMAP) at Colorado State University (CSU) is addressing this problem through a revolutionary new approach to representing cloud processes on their native scales, including the cloud-scale interaction processes that are active in cloud systems. CMMAP has set ambitious education and human-resource goals to share basic information about the atmosphere, clouds, weather, climate, and modeling with diverse K-12 and public audiences. This is accomplished through collaborations in resource development and dissemination between CMMAP scientists, CSU’s Little Shop of Physics (LSOP) program, and the Windows to the Universe (W2U) program at University Corporation for Atmospheric Research (UCAR). Little Shop of Physics develops new hands on science activities demonstrating basic science concepts fundamental to understanding atmospheric characteristics, weather, and climate. Videos capture demonstrations of children completing these activities which are broadcast to school districts and public television programs. CMMAP and LSOP educators and scientists partner in teaching a summer professional development workshops for teachers at CSU with a semester's worth of college-level content on the basic physics of the atmosphere, weather, climate, climate modeling, and climate change, as well as dozens of LSOP inquiry-based activities suitable for use in classrooms. The W2U project complements these efforts by developing and broadly disseminating new CMMAP-related online content pages, animations, interactives, image galleries, scientists’ biographies, and LSOP videos to K-12 and public audiences. Reaching nearly 20 million users annually, W2U is highly valued as a curriculum enhancement

  16. Modeling ozone and aerosol formation and transport in the pacific northwest with the community Multi-Scale Air Quality (CMAQ) modeling system.

    PubMed

    O'Neill, Susan M; Lamb, Brian K; Chen, Jack; Claiborn, Candis; Finn, Dennis; Otterson, Sally; Figueroa, Cristiana; Bowman, Clint; Boyer, Mike; Wilson, Rob; Arnold, Jeff; Aalbers, Steven; Stocum, Jeffrey; Swab, Christopher; Stoll, Matt; Dubois, Mike; Anderson, Mary

    2006-02-15

    The Community Multi-Scale Air Quality (CMAQ) modeling system was used to investigate ozone and aerosol concentrations in the Pacific Northwest (PNW) during hot summertime conditions during July 1-15, 1996. Two emission inventories (El) were developed: emissions for the first El were based upon the National Emission Trend 1996 (NET96) database and the BEIS2 biogenic emission model, and emissions for the second El were developed through a "bottom up" approach that included biogenic emissions obtained from the GLOBEIS model. The two simulations showed that elevated PM2.5 concentrations occurred near and downwind of the Interstate-5 corridor along the foothills of the Cascade Mountains and in forested areas of central Idaho. The relative contributions of organic and inorganic aerosols varied by region, but generally organic aerosols constituted the largest fraction of PM2.5. In wilderness areas near the 1-5 corridor, organic carbon from anthropogenic sources contributed approximately 50% of the total organic carbon with the remainder from biogenic precursors, while in wilderness areas in Idaho, biogenic organic carbon accounted for 80% of the total organic aerosol. Regional analysis of the secondary organic aerosol formation in the Columbia River Gorge, Central Idaho, and the Olympics/Puget Sound showed that the production rate of secondary organic carbon depends on local terpene concentrations and the local oxidizing capacity of the atmosphere, which was strongly influenced by anthropogenic emissions. Comparison with observations from 12 IMPROVE sites and 21 ozone monitoring sites showed that results from the two El simulations generally bracketed the average observed PM parameters and that errors calculated for the model results were within acceptable bounds. Analysis across all statistical parameters indicated that the NW-AIRQUEST El solution performed better at predicting PM2.5, PM1, and beta(ext) even though organic carbon PM was over-predicted, and the NET96 El

  17. Multi-Scale Validation of a Nanodiamond Drug Delivery System and Multi-Scale Engineering Education

    ERIC Educational Resources Information Center

    Schwalbe, Michelle Kristin

    2010-01-01

    This dissertation has two primary concerns: (i) evaluating the uncertainty and prediction capabilities of a nanodiamond drug delivery model using Bayesian calibration and bias correction, and (ii) determining conceptual difficulties of multi-scale analysis from an engineering education perspective. A Bayesian uncertainty quantification scheme…

  18. Multi-scale biomarker evaluation of the toxicity of a commercial azo dye (Disperse Red 1) in an animal model, the freshwater cnidarian Hydra attenuata.

    PubMed

    de Jong, Laetitia; Pech, Nicolas; de Aragão Umbuzeiro, Gisela; Moreau, Xavier

    2016-06-01

    Acute (24 h, 48 h, 72 h) and chronic (7 days) tests have been performed to evaluate the effects of the commercial azo dye Disperse Red 1 (DR1) using various biomarkers in the freshwater invertebrate Hydra attenuata. Morphological changes have been selected to calculate ecotoxicological thresholds for sublethal and lethal DR1 concentrations. A multinomial logistic model showed that the probability of each morphological stage occurrence was function of concentration, time and interaction between both. Results of oxidative balance parameter measurements (72 h and 7 days) suggest that polyps set up defense mechanisms to limit lipid peroxidation caused by DR1. DR1 exposure at hormetic concentrations induces increase of asexual reproductive rates. This result suggests (1) an impact on the fitness-related phenotypical traits and (2) trade-offs between reproduction and maintenance to allow the population to survive harsher conditions. Changes in serotonin immuno-labeling in polyps showing alterations in feeding behavior suggest that chronic DR1 exposure impaired neuronal processes related to ingesting behavior in H. attenuata. This ecotoxicity study sheds light on the possible serotonin function in Hydra model and reports for the first time that serotonin could play a significant role in feeding behavior. This study used a multi-scale biomarker approach investigating biochemical, morphological, reproductive and behavioral endpoints in Hydra attenuata. This organism is proposed for a pertinent animal model to assess ecotoxicological impact of pollutant mixtures in freshwater environment.

  19. From systems biology to photosynthesis and whole-plant physiology: a conceptual model for integrating multi-scale networks.

    PubMed

    Weston, David J; Hanson, Paul J; Norby, Richard J; Tuskan, Gerald A; Wullschleger, Stan D

    2012-02-01

    Network analysis is now a common statistical tool for molecular biologists. Network algorithms are readily used to model gene, protein and metabolic correlations providing insight into pathways driving biological phenomenon. One output from such an analysis is a candidate gene list that can be responsible, in part, for the biological process of interest. The question remains, however, as to whether molecular network analysis can be used to inform process models at higher levels of biological organization. In our previous work, transcriptional networks derived from three plant species were constructed, interrogated for orthology and then correlated with photosynthetic inhibition at elevated temperature. One unique aspect of that study was the link from co-expression networks to net photosynthesis. In this addendum, we propose a conceptual model where traditional network analysis can be linked to whole-plant models thereby informing predictions on key processes such as photosynthesis, nutrient uptake and assimilation, and C partitioning.

  20. A comprehensively quantitative method of evaluating the impact of drought on crop yield using daily multi-scale SPEI and crop growth process model

    NASA Astrophysics Data System (ADS)

    Wang, Qianfeng; Wu, Jianjun; Li, Xiaohan; Zhou, Hongkui; Yang, Jianhua; Geng, Guangpo; An, Xueli; Liu, Leizhen; Tang, Zhenghong

    2016-11-01

    The quantitative evaluation of the impact of drought on crop yield is one of the most important aspects in agricultural water resource management. To assess the impact of drought on wheat yield, the Environmental Policy Integrated Climate (EPIC) crop growth model and daily Standardized Precipitation Evapotranspiration Index (SPEI), which is based on daily meteorological data, are adopted in the Huang Huai Hai Plain. The winter wheat crop yields are estimated at 28 stations, after calibrating the cultivar coefficients based on the experimental site data, and SPEI data was taken 11 times across the growth season from 1981 to 2010. The relationship between estimated yield and multi-scale SPEI were analyzed. The optimum time scale SPEI to monitor drought during the crop growth period was determined. The reference yield was determined by averaging the yields from numerous non-drought years. From this data, we propose a comprehensive quantitative method which can be used to predict the impact of drought on wheat yields by combining the daily multi-scale SPEI and crop growth process model. This method was tested in the Huang Huai Hai Plain. The results suggested that estimation of calibrated EPIC was a good predictor of crop yield in the Huang Huai Hai Plain, with lower RMSE (15.4 %) between estimated yield and observed yield at six agrometeorological stations. The soil moisture at planting time was affected by the precipitation and evapotranspiration during the previous 90 days (about 3 months) in the Huang Huai Hai Plain. SPEIG90 was adopted as the optimum time scale SPEI to identify the drought and non-drought years, and identified a drought year in 2000. The water deficit in the year 2000 was significant, and the rate of crop yield reduction did not completely correspond with the volume of water deficit. Our proposed comprehensive method which quantitatively evaluates the impact of drought on crop yield is reliable. The results of this study further our understanding

  1. A comprehensively quantitative method of evaluating the impact of drought on crop yield using daily multi-scale SPEI and crop growth process model.

    PubMed

    Wang, Qianfeng; Wu, Jianjun; Li, Xiaohan; Zhou, Hongkui; Yang, Jianhua; Geng, Guangpo; An, Xueli; Liu, Leizhen; Tang, Zhenghong

    2017-04-01

    The quantitative evaluation of the impact of drought on crop yield is one of the most important aspects in agricultural water resource management. To assess the impact of drought on wheat yield, the Environmental Policy Integrated Climate (EPIC) crop growth model and daily Standardized Precipitation Evapotranspiration Index (SPEI), which is based on daily meteorological data, are adopted in the Huang Huai Hai Plain. The winter wheat crop yields are estimated at 28 stations, after calibrating the cultivar coefficients based on the experimental site data, and SPEI data was taken 11 times across the growth season from 1981 to 2010. The relationship between estimated yield and multi-scale SPEI were analyzed. The optimum time scale SPEI to monitor drought during the crop growth period was determined. The reference yield was determined by averaging the yields from numerous non-drought years. From this data, we propose a comprehensive quantitative method which can be used to predict the impact of drought on wheat yields by combining the daily multi-scale SPEI and crop growth process model. This method was tested in the Huang Huai Hai Plain. The results suggested that estimation of calibrated EPIC was a good predictor of crop yield in the Huang Huai Hai Plain, with lower RMSE (15.4 %) between estimated yield and observed yield at six agrometeorological stations. The soil moisture at planting time was affected by the precipitation and evapotranspiration during the previous 90 days (about 3 months) in the Huang Huai Hai Plain. SPEIG90 was adopted as the optimum time scale SPEI to identify the drought and non-drought years, and identified a drought year in 2000. The water deficit in the year 2000 was significant, and the rate of crop yield reduction did not completely correspond with the volume of water deficit. Our proposed comprehensive method which quantitatively evaluates the impact of drought on crop yield is reliable. The results of this study further our

  2. Multi-scale defect interactions in high-rate brittle material failure. Part I: Model formulation and application to ALON

    NASA Astrophysics Data System (ADS)

    Tonge, Andrew L.; Ramesh, K. T.

    2016-01-01

    Within this two part series we develop a new material model for ceramic protection materials to provide an interface between microstructural parameters and bulk continuum behavior to provide guidance for materials design activities. Part I of this series focuses on the model formulation that captures the strength variability and strain rate sensitivity of brittle materials and presents a statistical approach to assigning the local flaw distribution within a specimen. The material model incorporates a Mie-Grüneisen equation of state, micromechanics based damage growth, granular flow and dilatation of the highly damaged material, and pore compaction for the porosity introduced by granular flow. To provide initial qualitative validation and illustrate the usefulness of the model, we use the model to investigate Edge on Impact experiments (Strassburger, 2004) on Aluminum Oxynitride (AlON), and discuss the interactions of multiple mechanisms during such an impact event. Part II of this series is focused on additional qualitative validation and using the model to suggest material design directions for boron carbide.

  3. Population Estimation Using a 3D City Model: A Multi-Scale Country-Wide Study in the Netherlands

    PubMed Central

    Arroyo Ohori, Ken; Ledoux, Hugo; Peters, Ravi; Stoter, Jantien

    2016-01-01

    The remote estimation of a region’s population has for decades been a key application of geographic information science in demography. Most studies have used 2D data (maps, satellite imagery) to estimate population avoiding field surveys and questionnaires. As the availability of semantic 3D city models is constantly increasing, we investigate to what extent they can be used for the same purpose. Based on the assumption that housing space is a proxy for the number of its residents, we use two methods to estimate the population with 3D city models in two directions: (1) disaggregation (areal interpolation) to estimate the population of small administrative entities (e.g. neighbourhoods) from that of larger ones (e.g. municipalities); and (2) a statistical modelling approach to estimate the population of large entities from a sample composed of their smaller ones (e.g. one acquired by a government register). Starting from a complete Dutch census dataset at the neighbourhood level and a 3D model of all 9.9 million buildings in the Netherlands, we compare the population estimates obtained by both methods with the actual population as reported in the census, and use it to evaluate the quality that can be achieved by estimations at different administrative levels. We also analyse how the volume-based estimation enabled by 3D city models fares in comparison to 2D methods using building footprints and floor areas, as well as how it is affected by different levels of semantic detail in a 3D city model. We conclude that 3D city models are useful for estimations of large areas (e.g. for a country), and that the 3D approach has clear advantages over the 2D approach. PMID:27254151

  4. A Multi-scale Thermomechanical-Solidification Model to Simulate the Transient Force Field Deforming an Aluminum 6061 Semisolid Weld

    NASA Astrophysics Data System (ADS)

    Zareie Rajani, H. R.; Phillion, A. B.

    2015-08-01

    Formation of hot cracks is strongly affected by the transient force field acting on the semisolid weld-base metal interface. This paper presents a model that numerically simulates such a transient force field as a function of welding parameters. The model consists of two modules: (1) By means of a granular model of solidification, the microstructure of the semisolid area within the weld is reconstructed in three dimensions; (2) Since the transient force field is developed through the mechanical interaction between the semisolid weld and its base metal, the mechanical response of the base metal to the solidification of the weld is then simulated through finite element analysis. The results show that changing welding parameters and welding constraints varies the transient force field. Based on the obtained force fields, a qualitative study is also conducted to predict the susceptibility of various welds to hot cracking.

  5. Insights and Challenges of Multi-Scale Modeling of Sarcomere Mechanics in cTn and Tm DCM Mutants—Genotype to Cellular Phenotype

    PubMed Central

    Dewan, Sukriti; McCabe, Kimberly J.; Regnier, Michael; McCulloch, Andrew D.

    2017-01-01

    Dilated Cardiomyopathy (DCM) is a leading cause of sudden cardiac death characterized by impaired pump function and dilatation of cardiac ventricles. In this review we discuss various in silico approaches to elucidating the mechanisms of genetic mutations leading to DCM. The approaches covered in this review focus on bridging the spatial and temporal gaps that exist between molecular and cellular processes. Mutations in sarcomeric regulatory thin filament proteins such as the troponin complex (cTn) and Tropomyosin (Tm) have been associated with DCM. Despite the experimentally-observed myofilament measures of contractility in the case of these mutations, the mechanisms by which the underlying molecular changes and protein interactions scale up to organ failure by these mutations remains elusive. The review highlights multi-scale modeling approaches and their applicability to study the effects of sarcomeric gene mutations in-silico. We discuss some of the insights that can be gained from computational models of cardiac biomechanics when scaling from molecular states to cellular level. PMID:28352236

  6. Pro-arrhythmogenic effects of CACNA1C G1911R mutation in human ventricular tachycardia: insights from cardiac multi-scale models

    PubMed Central

    Bai, Jieyun; Wang, Kuanquan; Li, Qince; Yuan, Yongfeng; Zhang, Henggui

    2016-01-01

    Mutations in the CACNA1C gene are associated with ventricular tachycardia (VT). Although the CACNA1C mutations were well identified in patients with cardiac arrhythmias, mechanisms by which cardiac arrhythmias are generated in such genetic mutation conditions remain unclear. In this study, we identified a novel mechanism of VT resulted from enhanced repolarization dispersion which is a key factor for arrhythmias in the CACNA1C G1911R mutation using multi-scale computational models of the human ventricle. The increased calcium influx in the mutation prolonged action potential duration (APD), produced steepened action potential duration restitution (APDR) curves as well as augmented membrane potential differences among different cell types during repolarization, increasing transmural dispersion of repolarization (DOR) and the spatial and temporal heterogeneity of cardiac electrical activities. Consequentially, the vulnerability to unidirectional conduction block in response to a premature stimulus increased at tissue level in the G1911R mutation. The increased functional repolarization dispersion anchored reentrant excitation waves in tissue and organ models, facilitating the initiation and maintenance of VT due to less meandering rotor tip. Thus, the increased repolarization dispersion caused by the G1911R mutation is a primary factor that may primarily contribute to the genesis of cardiac arrhythmias in Timothy Syndrome. PMID:27502440

  7. Multi-scale groundwater flow modeling during temperate climate conditions for the safety assessment of the proposed high-level nuclear waste repository site at Forsmark, Sweden

    NASA Astrophysics Data System (ADS)

    Joyce, Steven; Hartley, Lee; Applegate, David; Hoek, Jaap; Jackson, Peter

    2014-09-01

    Forsmark in Sweden has been proposed as the site of a geological repository for spent high-level nuclear fuel, to be located at a depth of approximately 470 m in fractured crystalline rock. The safety assessment for the repository has required a multi-disciplinary approach to evaluate the impact of hydrogeological and hydrogeochemical conditions close to the repository and in a wider regional context. Assessing the consequences of potential radionuclide releases requires quantitative site-specific information concerning the details of groundwater flow on the scale of individual waste canister locations (1-10 m) as well as details of groundwater flow and composition on the scale of groundwater pathways between the facility and the surface (500 m to 5 km). The purpose of this article is to provide an illustration of multi-scale modeling techniques and the results obtained when combining aspects of local-scale flows in fractures around a potential contaminant source with regional-scale groundwater flow and transport subject to natural evolution of the system. The approach set out is novel, as it incorporates both different scales of model and different levels of detail, combining discrete fracture network and equivalent continuous porous medium representations of fractured bedrock.

  8. Multi-Scale Computational Analyses of JP-8 Fuel Droplets and Vapors in Human Respiratory Airway Models

    DTIC Science & Technology

    2007-10-31

    micron- and nano-size aerosols in representative human nasal airways; (ii) multi- component and/or impure droplet evaporation or hygroscopity; (iii...14 1.3.4 Evaporation and deposition of multi- component droplets...fuel surrogate in order to track at least 12 components , i.e., chemical markers, considered to be most harmful. 20080226474 (iv) Model development and

  9. A multi-scale model for texture development in Zr/Nb nanolayered composites processed by accumulative roll bonding

    NASA Astrophysics Data System (ADS)

    Ardeljan, M.; Knezevic, M.; Nizolek, T.; Beyerlein, I. J.; Zheng, S. J.; Carpenter, J. S.; McCabe, R. J.; Mara, N. A.; Pollock, T. M.

    2014-08-01

    Recently it has been demonstrated that nanolayered hcp/bcc Zr/Nb composites can be fabricated with a severe plastic deformation technique called accumulative roll bonding (ARB) [1]. The final layer thickness averaged to approximately 90 nm for both phases. Interestingly, the texture measurements show that the textures in each phase correspond to those of rolled single-phase rolled Zr and Nb for a wide range of layer thickness from the micron to the nanoscales. This is in remarkable contrast to fcc/bcc Cu/Nb layered composites made by the same ARB technique, which developed textures that strongly deviated from theoretical rolling textures of Cu or Nb alone when the layers were refined to submicron and nanoscale dimensions. To model texture evolution and reveal the underlying deformation mechanisms, we developed a 3D multiscale model that combines crystal plasticity finite element with a thermally activated dislocation density based hardening law [2]. For systematic study, the model is applied to a two-phase Zr/Nb polycrystalline laminate and to the same polycrystalline Zr and polycrystalline Nb as single-phase metals. Consistent with the measurement, the model predicts that texture evolution in the phases in the composite and the relative activities of the hcp slip modes are very similar to those in the phases in monolithic form. In addition, the two-phase model also finds that no through-thickness texture gradient develops. This result suggests that neither the nanoscale grain sizes nor the bimetal Zr/Nb interfaces induce deformation mechanisms different from those at the coarse-grain scale.

  10. Enhancement of denitrification in permeable carbonate sediment due to intra-granular porosity: A multi-scale modelling analysis

    NASA Astrophysics Data System (ADS)

    Kessler, Adam J.; Cardenas, M. Bayani; Santos, Isaac R.; Cook, Perran L. M.

    2014-09-01

    It has recently been hypothesized that bulk denitrification rates in carbonate sands may be enhanced by reactions occurring in the intra-granular pores, cracks and crevices. We tested this hypothesis using a series of flow and reactive transport models spanning from the pore-scale (∼mm) to the continuum scales (∼10 cm bedforms). Pore-scale simulations solved the coupled Navier-Stokes and Brinkman equations and represented flow-through reactor experiments previously performed on coral reef sands. The results revealed that intra-granular transport and reactions can explain over-all denitrification enhancement. A sensitivity study with a single grain diffusive transport model showed that in the majority of cases, the resultant increase in denitrification was not coupled to nitrification within a single grain. Only for large grain diameters of 2 and 4 mm was coupled nitrification-denitrification important. In most cases, coupled nitrification-denitrification instead arose as conditions became more reducing along a flow path, as is the case in quartz sands without intragranular pores. An intra-granular reaction rate based on a single grain model was incorporated into a continuum-scale Darcy flow and reactive transport model for a rippled sand bed, where porewater flow is driven by the turbulent current over the ripple. The results of the Darcy-scale model suggest that intra-granular pores increase the amount of slow-flowing areas within which coupled nitrification-denitrification can occur. We conclude that the complex advective flow field does not strongly inhibit denitrification enhancement by carbonate sand grains, as it does in silica sands. Thus, intra-granular reactions may enhance bulk denitrification in carbonate sediment with porous grains under natural advective conditions.

  11. Multi-scale modelling for the assessment of water quality and land subsidence due to salt layers dissolution

    NASA Astrophysics Data System (ADS)

    Gourdier, Sébastien; Bazargan-Sabet, Behrooz; Quang Vong, Chan

    2016-04-01

    Long term evolution of salt mine depends on mechanical behavior of the material but also on specific conditions like the intrusion of water into working areas. Such phenomenon has been observed in the Nancy Basin (East of France) where brine percolates through access shafts accompanied by significant subsidence at the surface level, bringing about growing societal concerns. In order to understand the mechanisms and kinetics of dissolution of salt inducing the phenom-enon of subsidence, a numerical model is implemented. The circulation of water between the salt layer and the impervious layer induces the creation of dissolution channels. In active disso-lution zones, the channel network constantly evolves: new channels appear with new dissolution zones while others collapse because of their too important dimensions. The model simulates the phenomenon of dissolution at the channel scale first, then at the basin scale. Dissolution channels modeling has been realized using COMSOL Multiphysics® with Darcy's Law and Solute Transport interfaces. At the channel scale, realistic parameters used as input data gave raise to output results con-sistent with the expected range of values for numerical assessment of the transient period and mass fluxes. At the basin scale, initial porosity and hydraulic conductivity fields, related to each other by a cubic law, are assumed to follow a Weibull distribution. From this initial state, the transient model calculates the evolution of porosity with time, taking into account Darcy's velocity as it was formulated by Yao et al. (2014). Progress in dissolution and transport gives rise to the creation of dissolution channels. Channels mechanical behavior is investigated through extending 2D model into 3D one. The calculations show that open channels collapse when they reach a width of approximatively one meter. The results of these investigations are consistent with the in situ measurements, notably with the estimation of the subsidence rate

  12. Multi-scale model of the ionosphere from the combination of modern space-geodetic satellite techniques - project status and first results

    NASA Astrophysics Data System (ADS)

    Schmidt, M.; Hugentobler, U.; Jakowski, N.; Dettmering, D.; Liang, W.; Limberger, M.; Wilken, V.; Gerzen, T.; Hoque, M.; Berdermann, J.

    2012-04-01

    Near real-time high resolution and high precision ionosphere models are needed for a large number of applications, e.g. in navigation, positioning, telecommunications or astronautics. Today these ionosphere models are mostly empirical, i.e., based purely on mathematical approaches. In the DFG project 'Multi-scale model of the ionosphere from the combination of modern space-geodetic satellite techniques (MuSIK)' the complex phenomena within the ionosphere are described vertically by combining the Chapman electron density profile with a plasmasphere layer. In order to consider the horizontal and temporal behaviour the fundamental target parameters of this physics-motivated approach are modelled by series expansions in terms of tensor products of localizing B-spline functions depending on longitude, latitude and time. For testing the procedure the model will be applied to an appropriate region in South America, which covers relevant ionospheric processes and phenomena such as the Equatorial Anomaly. The project connects the expertise of the three project partners, namely Deutsches Geodätisches Forschungsinstitut (DGFI) Munich, the Institute of Astronomical and Physical Geodesy (IAPG) of the Technical University Munich (TUM) and the German Aerospace Center (DLR), Neustrelitz. In this presentation we focus on the current status of the project. In the first year of the project we studied the behaviour of the ionosphere in the test region, we setup appropriate test periods covering high and low solar activity as well as winter and summer and started the data collection, analysis, pre-processing and archiving. We developed partly the mathematical-physical modelling approach and performed first computations based on simulated input data. Here we present information on the data coverage for the area and the time periods of our investigations and we outline challenges of the multi-dimensional mathematical-physical modelling approach. We show first results, discuss problems

  13. A multi-scale problem arising in a model of avian flu virus in a seabird colony

    NASA Astrophysics Data System (ADS)

    Clancy, C. F.; O'Callaghan, M. J. A.; Kelly, T. C.

    2006-12-01

    Understanding the dynamics of epidemics of novel pathogens such as the H5N1 strain of avian influenza is of crucial importance to public and veterinary health as well as wildlife ecology. We model the effect of a new virus on a seabird colony, where no pre-existing Herd Immunity exists. The seabirds in question are so-called K-strategists, i.e. they have a relatively long life expectancy and very low reproductive output. They live in isolated colonies which typically contain tens of thousands of birds. These densely populated colonies, with so many birds competing for nesting space, would seem to provide perfect conditions for the entry and spread of an infection. Yet there are relatively few reported cases of epidemics among these seabirds. We develop a SEIR model which incorporates some of the unusual features of seabird population biology and examine the effects of introducing a pathogen into the colony.

  14. Multi-scale Drivers of Variations in Atmospheric Evaporative Demand Based on Observations and Physically-based Modeling

    NASA Astrophysics Data System (ADS)

    Peng, L.; Sheffield, J.; Li, D.

    2015-12-01

    Evapotranspiration (ET) is a key link between the availability of water resources and climate change and climate variability. Variability of ET has important environmental and socioeconomic implications for managing hydrological hazards, food and energy production. Although there have been many observational and modeling studies of ET, how ET has varied and the drivers of the variations at different temporal scales remain elusive. Much of the uncertainty comes from the atmospheric evaporative demand (AED), which is the combined effect of radiative and aerodynamic controls. The inconsistencies among modeled AED estimates and the limited observational data may originate from multiple sources including the limited time span and uncertainties in the data. To fully investigate and untangle the intertwined drivers of AED, we present a spectrum analysis to identify key controls of AED across multiple temporal scales. We use long-term records of observed pan evaporation for 1961-2006 from 317 weather stations across China and physically-based model estimates of potential evapotranspiration (PET). The model estimates are based on surface meteorology and radiation derived from reanalysis, satellite retrievals and station data. Our analyses show that temperature plays a dominant role in regulating variability of AED at the inter-annual scale. At the monthly and seasonal scales, the primary control of AED shifts from radiation in humid regions to humidity in dry regions. Unlike many studies focusing on the spatial pattern of ET drivers based on a traditional supply and demand framework, this study underlines the importance of temporal scales when discussing controls of ET variations.

  15. Multi-Scale Behavioral Modeling and Analysis Promoting a Fundamental Understanding of Agent-Based System Design and Operation

    DTIC Science & Technology

    2007-03-01

    concept of heterogeneous agents where agents are composed of various combinations of Core Competencies. 7 Electrical circuit designers are guided...current*voltage). Circuit designers currently benefit from a wide range of tools to model designs (transistor designs) such that the design...intended to provide for MAS designers what circuit designers now enjoy – understanding of the first principles of MAS behaviors and the ability to design

  16. Predicting cell viability within tissue scaffolds under equiaxial strain: multi-scale finite element model of collagen-cardiomyocytes constructs.

    PubMed

    Elsaadany, Mostafa; Yan, Karen Chang; Yildirim-Ayan, Eda

    2017-01-16

    Successful tissue engineering and regenerative therapy necessitate having extensive knowledge about mechanical milieu in engineered tissues and the resident cells. In this study, we have merged two powerful analysis tools, namely finite element analysis and stochastic analysis, to understand the mechanical strain within the tissue scaffold and residing cells and to predict the cell viability upon applying mechanical strains. A continuum-based multi-length scale finite element model (FEM) was created to simulate the physiologically relevant equiaxial strain exposure on cell-embedded tissue scaffold and to calculate strain transferred to the tissue scaffold (macro-scale) and residing cells (micro-scale) upon various equiaxial strains. The data from FEM were used to predict cell viability under various equiaxial strain magnitudes using stochastic damage criterion analysis. The model validation was conducted through mechanically straining the cardiomyocyte-encapsulated collagen constructs using a custom-built mechanical loading platform (EQUicycler). FEM quantified the strain gradients over the radial and longitudinal direction of the scaffolds and the cells residing in different areas of interest. With the use of the experimental viability data, stochastic damage criterion, and the average cellular strains obtained from multi-length scale models, cellular viability was predicted and successfully validated. This methodology can provide a great tool to characterize the mechanical stimulation of bioreactors used in tissue engineering applications in providing quantification of mechanical strain and predicting cellular viability variations due to applied mechanical strain.

  17. Multi-scale reservoir modeling as an integrated assessment tool for geo-sequestration in the San Juan Basin

    USGS Publications Warehouse

    Young, G.; Haerer, D.; Bromhal, G.; Reeves, S.

    2007-01-01

    The Southwestern Regional Partnership on CO2 Sequestration conducted an Enhanced Coalbed Methane (ECBM)/Carbon Storage Pilot in the San Juan Basin as part of the ongoing DOE/NETL Carbon Capture and Storage Program. The primary goal of this pilot is to demonstrate the efficacy of using CO2 to enhance coalbed methane recovery particularly near reservoir abandonment pressure while also evaluating the suitability of coal seams for longer-term carbon storage. Basic geologic models of the coal seams were developed from well logs in the area. Production histories from several surrounding CBM wells were shown. To monitor the injection of up to 75,000 ton of CO2 beginning September 2007, seismic surveys and tiltmeter arrays were utilized. Larger-scale geo-hydrodynamic simulations were used to develop a regional model for the fluid dynamics of the northern San Juan Basin. Smaller-scale reservoir simulations, incorporating available laboratory and field data, were used to develop an improved understanding of reservoir dynamics within the specific 640-acre pilot area. Both modeling scales were critical to assessing the suitability of deploying commercial carbon storage programs throughout the basin. Reservoir characterization results on the optimization of total CO2 injection volume, injection rate over time, and how CO2 is expected to disperse after injection are presented. This is an abstract of a paper presented at the 2007 AIChE Annual Meeting (Salt Lake City, UT 11/4-9/2007).

  18. Data-driven modeling of hydroclimatic trends and soil moisture: Multi-scale data integration and decision support

    NASA Astrophysics Data System (ADS)

    Coopersmith, Evan Joseph

    The techniques and information employed for decision-making vary with the spatial and temporal scope of the assessment required. In modern agriculture, the farm owner or manager makes decisions on a day-to-day or even hour-to-hour basis for dozens of fields scattered over as much as a fifty-mile radius from some central location. Following precipitation events, land begins to dry. Land-owners and managers often trace serpentine paths of 150+ miles every morning to inspect the conditions of their various parcels. His or her objective lies in appropriate resource usage -- is a given tract of land dry enough to be workable at this moment or would he or she be better served waiting patiently? Longer-term, these owners and managers decide upon which seeds will grow most effectively and which crops will make their operations profitable. At even longer temporal scales, decisions are made regarding which fields must be acquired and sold and what types of equipment will be necessary in future operations. This work develops and validates algorithms for these shorter-term decisions, along with models of national climate patterns and climate changes to enable longer-term operational planning. A test site at the University of Illinois South Farms (Urbana, IL, USA) served as the primary location to validate machine learning algorithms, employing public sources of precipitation and potential evapotranspiration to model the wetting/drying process. In expanding such local decision support tools to locations on a national scale, one must recognize the heterogeneity of hydroclimatic and soil characteristics throughout the United States. Machine learning algorithms modeling the wetting/drying process must address this variability, and yet it is wholly impractical to construct a separate algorithm for every conceivable location. For this reason, a national hydrological classification system is presented, allowing clusters of hydroclimatic similarity to emerge naturally from annual

  19. Multi-Scale Particle Size Distributions of Mars, Moon and Itokawa based on a time-maturation dependent fragmentation model

    NASA Astrophysics Data System (ADS)

    Charalambous, C. A.; Pike, W. T.

    2013-12-01

    We present the development of a soil evolution framework and multiscale modelling of the surface of Mars, Moon and Itokawa thus providing an atlas of extra-terrestrial Particle Size Distributions (PSD). These PSDs are profoundly based on a tailoring method which interconnects several datasets from different sites captured by the various missions. The final integrated product is then fully justified through a soil evolution analysis model mathematically constructed via fundamental physical principles (Charalambous, 2013). The construction of the PSD takes into account the macroscale fresh primary impacts and their products, the mesoscale distributions obtained by the in-situ data of surface missions (Golombek et al., 1997, 2012) and finally the microscopic scale distributions provided by Curiosity and Phoenix Lander (Pike, 2011). The distribution naturally extends at the magnitudinal scales at which current data does not exist due to the lack of scientific instruments capturing the populations at these data absent scales. The extension is based on the model distribution (Charalambous, 2013) which takes as parameters known values of material specific probabilities of fragmentation and grinding limits. Additionally, the establishment of a closed-form statistical distribution provides a quantitative description of the soil's structure. Consequently, reverse engineering of the model distribution allows the synthesis of soil that faithfully represents the particle population at the studied sites (Charalambous, 2011). Such representation essentially delivers a virtual soil environment to work with for numerous applications. A specific application demonstrated here will be the information that can directly be extracted for the successful drilling probability as a function of distance in an effort to aid the HP3 instrument of the 2016 Insight Mission to Mars. Pike, W. T., et al. "Quantification of the dry history of the Martian soil inferred from in situ microscopy

  20. Multi-scale First-Principles Modeling of Three-Phase System of Polymer Electrolyte Membrane Fuel Cel

    SciTech Connect

    Brunello, Giuseppe; Choi, Ji; Harvey, David; Jang, Seung

    2012-07-01

    The three-phase system consisting of Nafion, graphite and platinum in the presence of water is studied using molecule dynamics simulation. The force fields describing the molecular interaction between the components in the system are developed to reproduce the energies calculated from density functional theory modeling. The configuration of such complicated three-phase system is predicted through MD simulations. The nanophase-segregation and transport properties are investigated from the equilibrium state. The coverage of the electrolyte on the platinum surface and the dissolution of oxygen are analyzed.

  1. Multi-scale, micro-computed tomography-based pore network models to simulate drainage in heterogeneous rocks

    NASA Astrophysics Data System (ADS)

    Bultreys, Tom; Van Hoorebeke, Luc; Cnudde, Veerle

    2015-04-01

    The multi-phase flow behavior of complex rocks with broad pore size distributions often digresses from classical relations. Pore-scale simulation methods can be a great tool to improve the understanding of this behavior. However, the broad range of pore sizes present makes it difficult to gather the experimental input data needed for these simulations and poses great computational challenges. We developed a novel micro-computed-tomography (micro-CT) based dual pore network model (DPNM), which takes microporosity into account in an upscaled fashion using symbolic network elements called micro-links, while treating the macroporosity as a traditional pore network model. The connectivity and conductivity of the microporosity is derived from local information measured on micro-CT scans. Microporous connectivity is allowed both in parallel and in series to the macropore network. We allow macropores to be drained as a consequence of their connection with microporosity, permitting simulations where the macropore network alone does not percolate. The validity of the method is shown by treating an artificial network and a network extracted from a micro-CT scan of Estaillades limestone.

  2. Experimentally- and Dislocation-Based Multi-scale Modeling of Metal Plasticity Including Temperature and Rate Effects

    NASA Astrophysics Data System (ADS)

    Nemat-Nasser, Sia

    2005-08-01

    Excluding high-temperature creep, the plastic deformation of metals occurs by the motion of dislocations that produce slip on various slip planes in various slip directions. It is thus natural to seek to develop constitutive relations for metal plasticity, based on the concept of dislocations and their kinematics and kinetics. Such an approach has been successfully used by a number of investigators over the past several decades. More recently, however, the development of the recovery Hopkinson techniques by this writer and his coworkers at UCSD's CEAM, has provided important experimental tools to obtain reliable data on stress-strain response of variety of metals over broad ranges of strain rates and temperatures. A wealth of information has become available to guide and verify constitutive models that are proposed to describe metal plasticity. Using such data, I have been able to create a class of dislocation-based models that involve a few material constants, and seem to accurately characterize the response of a large number of metals over 10-4 to 105/s strain rates, and 77 to 1,300K temperatures.

  3. New insights into low-temperature oxidation of propane from synchrotron photoionization mass spectrometry and multi-scale informatics modeling

    SciTech Connect

    Welz, Oliver; Burke, Michael P.; Antonov, Ivan O.; Goldsmith, C. Franklin; Savee, John David; Osborn, David L.; Taatjes, Craig A.; Klippenstein, Stephen J.; Sheps, Leonid

    2015-04-10

    We studied low-temperature propane oxidation at P = 4 Torr and T = 530, 600, and 670 K by time-resolved multiplexed photoionization mass spectrometry (MPIMS), which probes the reactants, intermediates, and products with isomeric selectivity using tunable synchrotron vacuum UV ionizing radiation. The oxidation is initiated by pulsed laser photolysis of oxalyl chloride, (COCl)2, at 248 nm, which rapidly generates a ~1:1 mixture of 1-propyl (n-propyl) and 2-propyl (i-propyl) radicals via the fast Cl + propane reaction. At all three temperatures, the major stable product species is propene, formed in the propyl + O2 reactions by direct HO2 elimination from both n- and i-propyl peroxy radicals. The experimentally derived propene yields relative to the initial concentration of Cl atoms are (20 ± 4)% at 530 K, (55 ± 11)% at 600 K, and (86 ± 17)% at 670 K at a reaction time of 20 ms. The lower yield of propene at low temperature reflects substantial formation of propyl peroxy radicals, which do not completely decompose on the experimental time scale. In addition, C3H6O isomers methyloxirane, oxetane, acetone, and propanal are detected as minor products. Our measured yields of oxetane and methyloxirane, which are coproducts of OH radicals, suggest a revision of the OH formation pathways in models of low-temperature propane oxidation. The experimental results are modeled and interpreted using a multiscale informatics approach, presented in detail in a separate publication (Burke, M. P.; Goldsmith, C. F.; Klippenstein, S. J.; Welz, O.; Huang H.; Antonov I. O.; Savee J. D.; Osborn D. L.; Zádor, J.; Taatjes, C. A.; Sheps, L. Multiscale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Reactions. J. Phys. Chem A. 2015, DOI: 10.1021/acs.jpca.5b01003). Additionally, we found that the model predicts the time profiles and yields of the experimentally observed primary products well

  4. New insights into low-temperature oxidation of propane from synchrotron photoionization mass spectrometry and multi-scale informatics modeling

    DOE PAGES

    Welz, Oliver; Burke, Michael P.; Antonov, Ivan O.; ...

    2015-04-10

    We studied low-temperature propane oxidation at P = 4 Torr and T = 530, 600, and 670 K by time-resolved multiplexed photoionization mass spectrometry (MPIMS), which probes the reactants, intermediates, and products with isomeric selectivity using tunable synchrotron vacuum UV ionizing radiation. The oxidation is initiated by pulsed laser photolysis of oxalyl chloride, (COCl)2, at 248 nm, which rapidly generates a ~1:1 mixture of 1-propyl (n-propyl) and 2-propyl (i-propyl) radicals via the fast Cl + propane reaction. At all three temperatures, the major stable product species is propene, formed in the propyl + O2 reactions by direct HO2 elimination frommore » both n- and i-propyl peroxy radicals. The experimentally derived propene yields relative to the initial concentration of Cl atoms are (20 ± 4)% at 530 K, (55 ± 11)% at 600 K, and (86 ± 17)% at 670 K at a reaction time of 20 ms. The lower yield of propene at low temperature reflects substantial formation of propyl peroxy radicals, which do not completely decompose on the experimental time scale. In addition, C3H6O isomers methyloxirane, oxetane, acetone, and propanal are detected as minor products. Our measured yields of oxetane and methyloxirane, which are coproducts of OH radicals, suggest a revision of the OH formation pathways in models of low-temperature propane oxidation. The experimental results are modeled and interpreted using a multiscale informatics approach, presented in detail in a separate publication (Burke, M. P.; Goldsmith, C. F.; Klippenstein, S. J.; Welz, O.; Huang H.; Antonov I. O.; Savee J. D.; Osborn D. L.; Zádor, J.; Taatjes, C. A.; Sheps, L. Multiscale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Reactions. J. Phys. Chem A. 2015, DOI: 10.1021/acs.jpca.5b01003). Additionally, we found that the model predicts the time profiles and yields of the experimentally observed primary products well, and shows satisfactory agreement for products

  5. Multi-scale geospatial agroecosystem modeling: a case study on the influence of soil data resolution on carbon budget estimates

    SciTech Connect

    Zhang, Xuesong; Sahajpal, Ritvik; Manowitz, D.; Zhao, Kaiguang; LeDuc, Stephen D.; Xu, Min; Xiong, Wei; Zhang, Aiping; Izaurralde, Roberto C.; Thomson, Allison M.; West, Tristram O.; Post, W. M.

    2014-05-01

    The development of effective measures to stabilize atmospheric CO2 concentration and mitigate negative impacts of climate change requires accurate quantification of the spatial variation and magnitude of the terrestrial carbon (C) flux. However, the spatial pattern and strength of terrestrial C sinks and sources remain uncertain. In this study, we designed a spatially-explicit agroecosystem modeling system by integrating the Environmental Policy Integrated Climate (EPIC) model with multiple sources of geospatial and surveyed datasets (including crop type map, elevation, climate forcing, fertilizer application, tillage type and distribution, and crop planting and harvesting date), and applied it to examine the sensitivity of cropland C flux simulations to two widely used soil databases (i.e. State Soil Geographic-STATSGO of a scale of 1:250,000 and Soil Survey Geographic-SSURGO of a scale of 1:24,000) in Iowa, USA. To efficiently execute numerous EPIC runs resulting from the use of high resolution spatial data (56m), we developed a parallelized version of EPIC. Both STATSGO and SSURGO led to similar simulations of crop yields and Net Ecosystem Production (NEP) estimates at the State level. However, substantial differences were observed at the county and sub-county (grid) levels. In general, the fine resolution SSURGO data outperformed the coarse resolution STATSGO data for county-scale crop-yield simulation, and within STATSGO, the area-weighted approach provided more accurate results. Further analysis showed that spatial distribution and magnitude of simulated NEP were more sensitive to the resolution difference between SSURGO and STATSGO at the county or grid scale. For over 60% of the cropland areas in Iowa, the deviations between STATSGO- and SSURGO-derived NEP were larger than 1MgCha(-1)yr(-1), or about half of the average cropland NEP, highlighting the significant uncertainty in spatial distribution and magnitude of simulated C fluxes resulting from

  6. Integration of multi-source and multi-scale datasets for 3D structural modeling for subsurface exploration targeting, Luanchuan Mo-polymetallic district, China

    NASA Astrophysics Data System (ADS)

    Wang, Gongwen; Ma, Zhenbo; Li, Ruixi; Song, Yaowu; Qu, Jianan; Zhang, Shouting; Yan, Changhai; Han, Jiangwei

    2017-04-01

    In this paper, multi-source (geophysical, geochemical, geological and remote sensing) datasets were used to construct multi-scale (district-, deposit-, and orebody-scale) 3D geological models and extract 3D exploration criteria for subsurface Mo-polymetallic exploration targeting in the Luanchuan district in China. The results indicate that (i) a series of region-/district-scale NW-trending thrusts controlled main Mo-polymetallic forming, and they were formed by regional Indosinian Qinling orogenic events, the secondary NW-trending district-scale folds and NE-trending faults and the intrusive stock structure are produced based on thrust structure in Caledonian-Indosinian orogenic events; they are ore-bearing zones and ore-forming structures; (ii) the NW-trending district-scale and NE-trending deposit-scale normal faults were crossed and controlled by the Jurassic granite stocks in 3D space, they are associated with the magma-skarn Mo polymetallic mineralization (the 3D buffer distance of ore-forming granite stocks is 600 m) and the NW-trending hydrothermal Pb-Zn deposits which are surrounded by the Jurassic granite stocks and constrained by NW-trending or NE-trending faults (the 3D buffer distance of ore-forming fault is 700 m); and (iii) nine Mo polymetallic and four Pb-Zn targets were identified in the subsurface of the Luanchuan district.

  7. Evolution of Tides and Tidal Dissipation Over the Past 26,000 Years Using a Multi-Scale Model of Global Barotropic Tides

    NASA Astrophysics Data System (ADS)

    Salehipour, H.; Peltier, W. R.

    2014-12-01

    In this paper we will describe the results obtained through integration of a further refined version of the truly global barotropic tidal model of Salehipour et al. (Ocean Modell., 69, 2013) using the most recent reconstruction of ice-age bathymetric conditions as embodied in the recently constructed ICE-6G_C (VM5a) model of Peltier et al. (JGR-Solid Earth, in press, 2014). Our interest is in the spatial and temporal evolution of tidal amplitude, phase and dissipation from the Last Glacial Maximum (LGM) 26,000 years ago until the present. The state-of-the-art higher order nonlinear tidal model of Salehipour et al. (2013) includes a highly parallelized multi-scale framework in which an unstructured tessellation of the global ocean enables extensive local refinement around regions of interest such as the Hawaiian Ridge, the Brazil Basin and the Southern Ocean. At LGM, features such as the Patagonian Shelf were fully exposed land which during the deglaciation process would have been flooded leading to significant changes of tidal range along the evolving coastline. In the further development of this model we have included the fully iterated treatment of the influence of gravitational self-attraction and loading as in, e.g. Egbert et al. (JGR-Oceans, 109, 2004). The treatment of the dissipation of the barotropic tide through dissipation of the internal tide has also been significantly improved. Our paleobathymetry and coastline data sets extend from LGM to present at 500 year intervals and constitute a significant refinement of the widely employed ICE-5G (VM2) model of Peltier (Annu. Rev. Earth Planet. Sci., 32, 2004). Our results will be compared with those recently published by Green & Nycander (JPO, 43, 2013) and Wilmes & Green (JGR-Oceans, 119, 2014) as well as with the earlier results of Griffiths & Peltier (GRL, 35, 2008; J. Clim., 22, 2009).

  8. Multi-Scale Autoregressive Processes

    DTIC Science & Technology

    1989-06-01

    rationnelles et leurs langages," Mas- son 1984, Collection "Etudes et Recherches en Informatique". [12] J.L. DUNAU, "Etude d’une classe de marches...June 1989 LIDS-P-1880 Multi-Scale Autoregressive Processes Michele Basseville’ Albert Benveniste’ Institut de Recherche en Informatique et Systemes...Centre National de la Recherche Scientifique (CNRS) and A.B. is also with Institut National de Recherche en Informatique et en Automatique (INRIA). The

  9. Role of band 3 in the erythrocyte membrane structural changes under thermal fluctuations -multi scale modeling considerations.

    PubMed

    Pajic-Lijakovic, Ivana

    2015-12-01

    An attempt was made to discuss and connect various modeling approaches on various time and space scales which have been proposed in the literature in order to shed further light on the erythrocyte membrane rearrangement caused by the cortex-lipid bilayer coupling under thermal fluctuations. Roles of the main membrane constituents: (1) the actin-spectrin cortex, (2) the lipid bilayer, and (3) the trans membrane protein band 3 and their course-consequence relations were considered in the context of the cortex non linear stiffening and corresponding anomalous nature of energy dissipation. The fluctuations induce alternating expansion and compression of the membrane parts in order to ensure surface and volume conservation. The membrane structural changes were considered within two time regimes. The results indicate that the cortex non linear stiffening and corresponding anomalous nature of energy dissipation are related to the spectrin flexibility distribution and the rate of its changes. The spectrin flexibility varies from purely flexible to semi flexible. It is influenced by: (1) the number of band 3 molecules attached to single spectrin filaments, and (2) phosphorylation of the actin-junctions. The rate of spectrin flexibility changes depends on the band 3 molecules rearrangement.

  10. Multi-scale modelling of pulsed nanosecond dielectric barrier plasma discharges in plane-to-plane geometry

    NASA Astrophysics Data System (ADS)

    Nagaraja, Sharath; Yang, Vigor; Adamovich, Igor

    2013-04-01

    An integrated theoretical and numerical framework is developed to study the dynamics of energy coupling, gas heating and generation of active species by repetitively pulsed nanosecond dielectric barrier discharges (NS DBDs) in air. The work represents one of the first attempts to simulate, in a self-consistent manner, multiple (more than 100) nanosecond pulses. Detailed information is obtained about the electric-field transients during each voltage pulse, and accumulation of plasma generated species and gas heating over ms timescales. The plasma is modelled using a two-temperature, detailed chemistry scheme, with ions and neutral species in thermal equilibrium at the gas temperature, and electrons in thermal nonequilibrium. The analysis is conducted with pressures and pulsing frequency in the range 40-100 Torr and 1-105 Hz, respectively. The input electrical energy is directly proportional to the number density, and remains fairly constant on a per molecule basis from pulse to pulse. Repetitive pulsing results in uniform production of atomic oxygen in the discharge volume via electron-impact dissociation during voltage pulses, and through quenching of excited nitrogen molecules in the afterglow. The ion Joule effect causes rapid gas heating of ˜40 K/pulse in the cathode sheath and generates weak acoustic waves. Conductive heat loss to the walls during the time interval between voltage pulses prevents overheating of the cathode layer and development of ionization instabilities. A uniform ‘hat-shaped’ temperature profile develops in the discharge volume after multiple pulses, due to chemical heat release from quenching of excited species. This finding may explain experimentally observed volumetric ignition (as opposed to hot-spot ignition) in fuel-air mixtures subject to NS DBD.

  11. Integrating dynamic ecohydrological relations with the catchment response: A multi-scale hydrological modeling effort in a monsoonal regime basin

    NASA Astrophysics Data System (ADS)

    Mendez-Barroso, L. A.; Vivoni, E.; Robles-Morua, A.; Yepez, E. A.; Rodriguez, J. C.; Watts, C.; Saiz-Hernandez, J.

    2013-05-01

    Seasonal vegetation changes highly affect the energy and hydrologic fluxes in semiarid regions around the world. Accounting for different water use strategies among drought-deciduous ecosystems is important for understanding how these exploit the temporally brief and localized rainfall pulses of the North American Monsoon (NAM). Furthermore, quantifying these plant-water relations can help elucidate the spatial patterns of ecohydrological processes at catchment scale in the NAM region. In this effort, we focus on the San Miguel river basin (~ 3500 km2) in Sonora, Mexico, which exhibits seasonal vegetation greening that varies across ecosystems organized along mountain fronts. To assess the spatial variability of ecohydrological conditions, we relied on diverse tools that included multi-temporal remote sensing observations, model-based meteorological forcing, ground-based water and energy flux measurements and hydrologic simulations carried out at multiple scales. We evaluated the impact of seasonal vegetation dynamics on evapotranspiration (ET), its partitioning into soil evaporation (E) and plant transpiration (T), as well as their spatiotemporal patterns over the course of the NAM season. We utilized ground observations of soil moisture and evapotranspiration estimated by the eddy covariance method at two sites, as well as inferences of ET partitioning from stable isotope measurements, to test the numerical simulations. We found that ecosystem phenological differences lead to variations in the time to peak in transpiration during a season and in the overall seasonal ratio of transpiration to evapotranspiration (T/ET). A sensitivity analysis of the numerical simulations revealed that vegetation cover and the soil moisure threshold at which stomata close exert strong controls on the seasonal dominance of transpiration or evaporation. The dynamics of ET and its partitioning are then mapped spatially revealing that mountain front ecosystems utilize water differently

  12. Strategies of Eradicating Glioma Cells: A Multi-Scale Mathematical Model with MiR-451-AMPK-mTOR Control

    PubMed Central

    Kim, Yangjin; Powathil, Gibin; Kang, Hyunji; Trucu, Dumitru; Kim, Hyeongi; Lawler, Sean; Chaplain, Mark

    2015-01-01

    The cellular dispersion and therapeutic control of glioblastoma, the most aggressive type of primary brain cancer, depends critically on the migration patterns after surgery and intracellular responses of the individual cancer cells in response to external biochemical and biomechanical cues in the microenvironment. Recent studies have shown that a particular microRNA, miR-451, regulates downstream molecules including AMPK and mTOR to determine the balance between rapid proliferation and invasion in response to metabolic stress in the harsh tumor microenvironment. Surgical removal of main tumor is inevitably followed by recurrence of the tumor due to inaccessibility of dispersed tumor cells in normal brain tissue. In order to address this multi-scale nature of glioblastoma proliferation and invasion and its response to conventional treatment, we propose a hybrid model of glioblastoma that analyses spatio-temporal dynamics at the cellular level, linking individual tumor cells with the macroscopic behaviour of cell organization and the microenvironment, and with the intracellular dynamics of miR-451-AMPK-mTOR signaling within a tumour cell. The model identifies a key mechanism underlying the molecular switches between proliferative phase and migratory phase in response to metabolic stress and biophysical interaction between cells in response to fluctuating glucose levels in the presence of blood vessels (BVs). The model predicts that cell migration, therefore efficacy of the treatment, not only depends on oxygen and glucose availability but also on the relative balance between random motility and strength of chemoattractants. Effective control of growing cells near BV sites in addition to relocalization of invisible migratory cells back to the resection site was suggested as a way of eradicating these migratory cells. PMID:25629604

  13. Multi-scale modeling predicts a balance of tumor necrosis factor-α and interleukin-10 controls the granuloma environment during Mycobacterium tuberculosis infection.

    PubMed

    Cilfone, Nicholas A; Perry, Cory R; Kirschner, Denise E; Linderman, Jennifer J

    2013-01-01

    Interleukin-10 (IL-10) and tumor necrosis factor-α (TNF-α) are key anti- and pro-inflammatory mediators elicited during the host immune response to Mycobacterium tuberculosis (Mtb). Understanding the opposing effects of these mediators is difficult due to the complexity of processes acting across different spatial (molecular, cellular, and tissue) and temporal (seconds to years) scales. We take an in silico approach and use multi-scale agent based modeling of the immune response to Mtb, including molecular scale details for both TNF-α and IL-10. Our model predicts that IL-10 is necessary to modulate macrophage activation levels and to prevent host-induced tissue damage in a granuloma, an aggregate of cells that forms in response to Mtb. We show that TNF-α and IL-10 parameters related to synthesis, signaling, and spatial distribution processes control concentrations of TNF-α and IL-10 in a granuloma and determine infection outcome in the long-term. We devise an overall measure of granuloma function based on three metrics - total bacterial load, macrophage activation levels, and apoptosis of resting macrophages - and use this metric to demonstrate a balance of TNF-α and IL-10 concentrations is essential to Mtb infection control, within a single granuloma, with minimal host-induced tissue damage. Our findings suggest that a balance of TNF-α and IL-10 defines a granuloma environment that may be beneficial for both host and pathogen, but perturbing the balance could be used as a novel therapeutic strategy to modulate infection outcomes.

  14. Multi-scale enhancement of climate prediction over land by increasing the model sensitivity to vegetation variability in EC-Earth

    NASA Astrophysics Data System (ADS)

    Alessandri, Andrea; Catalano, Franco; De Felice, Matteo; Van Den Hurk, Bart; Doblas Reyes, Francisco; Boussetta, Souhail; Balsamo, Gianpaolo; Miller, Paul A.

    2016-10-01

    The EC-Earth earth system model has been recently developed to include the dynamics of vegetation. In its original formulation, vegetation variability is simply operated by the Leaf Area Index (LAI), which affects climate basically by changing the vegetation physiological resistance to evapotranspiration. This coupling has been found to have only a weak effect on the surface climate modeled by EC-Earth. In reality, the effective sub-grid vegetation fractional coverage will vary seasonally and at interannual time-scales in response to leaf-canopy growth, phenology and senescence. Therefore it affects biophysical parameters such as the albedo, surface roughness and soil field capacity. To adequately represent this effect in EC-Earth, we included an exponential dependence of the vegetation cover on the LAI. By comparing two sets of simulations performed with and without the new variable fractional-coverage parameterization, spanning from centennial (twentieth century) simulations and retrospective predictions to the decadal (5-years), seasonal and weather time-scales, we show for the first time a significant multi-scale enhancement of vegetation impacts in climate simulation and prediction over land. Particularly large effects at multiple time scales are shown over boreal winter middle-to-high latitudes over Canada, West US, Eastern Europe, Russia and eastern Siberia due to the implemented time-varying shadowing effect by tree-vegetation on snow surfaces. Over Northern Hemisphere boreal forest regions the improved representation of vegetation cover tends to correct the winter warm biases, improves the climate change sensitivity, the decadal potential predictability as well as the skill of forecasts at seasonal and weather time-scales. Significant improvements of the prediction of 2 m temperature and rainfall are also shown over transitional land surface hot spots. Both the potential predictability at decadal time-scale and seasonal-forecasts skill are enhanced over

  15. Multi-scale enhancement of climate prediction over land by increasing the model sensitivity to vegetation variability in EC-Earth

    NASA Astrophysics Data System (ADS)

    Alessandri, Andrea; Catalano, Franco; De Felice, Matteo; Van Den Hurk, Bart; Doblas Reyes, Francisco; Boussetta, Souhail; Balsamo, Gianpaolo; Miller, Paul

    2016-04-01

    The EC-Earth earth system model has been recently developed to include the dynamics of vegetation. In its original formulation, vegetation variability is simply operated by the Leaf Area Index (LAI), which affects climate basically by changing the vegetation physiological resistance to evapotranspiration. This coupling has been found to have only a weak effect on the surface climate modeled by EC-Earth. In reality, the effective sub-grid vegetation fractional coverage will vary seasonally and at interannual time-scales in response to leaf-canopy growth, phenology and senescence. Therefore it affects biophysical parameters such as the albedo, surface roughness and soil field capacity. To adequately represent this effect in EC-Earth, we included an exponential dependence of the vegetation cover on the LAI. By comparing two sets of simulations performed with and without the new variable fractional-coverage parameterization, spanning retrospective predictions at the decadal (5-years), seasonal and sub-seasonal time-scales, we show for the first time a significant multi-scale enhancement of vegetation impacts in climate simulation and prediction over land. Particularly large effects at multiple time scales are shown over boreal winter middle-to-high latitudes over Canada, West US, Eastern Europe, Russia and eastern Siberia due to the implemented time-varying shadowing effect by tree-vegetation on snow surfaces. Over Northern Hemisphere boreal forest regions the improved representation of vegetation cover tends to correct the winter warm biases, improves the climate change sensitivity, the decadal potential predictability as well as the skill of forecasts at seasonal and sub-seasonal time-scales. Significant improvements of the prediction of 2m temperature and rainfall are also shown over transitional land surface hot spots. Both the potential predictability at decadal time-scale and seasonal-forecasts skill are enhanced over Sahel, North American Great Plains, Nordeste

  16. Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

    PubMed Central

    2010-01-01

    Background New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation. Results We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order to integrate and visualize large volume of data, novel statistical and mathematical approaches have been developed to reduce the size of the data. To our knowledge, this is the first such tool developed that can visualize human genome in three-dimension. We describe here the major features of Genome3D and discuss our multi-scale data framework using a representative basic physical model. We then demonstrate many of the issues and benefits of multi-resolution data integration. Conclusions Genome3D is a software visualization tool that explores a wide range of structural genomic and epigenetic data. Data from various sources of differing scales can be integrated within a hierarchical framework that is easily adapted to new developments concerning the structure of the physical genome. In addition, our tool has a simple annotation mechanism to incorporate non-structural information. Genome3D is unique is its ability to manipulate large amounts of multi-resolution data from diverse sources to uncover complex and new structural relationships within the genome. PMID:20813045

  17. Study of Multi-Scale Cloud Processes Over the Tropical Western Pacific Using Cloud-Resolving Models Constrained by Satellite Data

    SciTech Connect

    Dudhia, Jimy

    2013-03-12

    Clouds in the tropical western Pacific are an integral part of the large scale environment. An improved understanding of the multi-scale structure of clouds and their interactions with the environment is critical to the ARM (Atmospheric Radiation Measurement) program for developing and evaluating cloud parameterizations, understanding the consequences of model biases, and providing a context for interpreting the observational data collected over the ARM Tropical Western Pacific (TWP) sites. Three-dimensional cloud resolving models (CRMs) are powerful tools for developing and evaluating cloud parameterizations. However, a significant challenge in using CRMs in the TWP is that the region lacks conventional data, so large uncertainty exists in defining the large-scale environment for clouds. This project links several aspects of the ARM program, from measurements to providing improved analyses, and from cloud-resolving modeling to climate-scale modeling and parameterization development, with the overall objective to improve the representations of clouds in climate models and to simulate and quantify resolved cloud effects on the large-scale environment. Our objectives will be achieved through a series of tasks focusing on the use of the Weather Research and Forecasting (WRF) model and ARM data. Our approach includes: -- Perform assimilation of COSMIC GPS radio occultation and other satellites products using the WRF Ensemble Kalman Filter assimilation system to represent the tropical large-scale environment at 36 km grid resolution. This high-resolution analysis can be used by the community to derive forcing products for single-column models or cloud-resolving models. -- Perform cloud-resolving simulations using WRF and its nesting capabilities, driven by the improved regional analysis and evaluate the simulations against ARM datasets such as from TWP-ICE to optimize the microphysics parameters for this region. A cirrus study (Mace and co-authors) already exists for

  18. Advancing Ecological Models to Compare Scale in Multi-Level Educational Change

    ERIC Educational Resources Information Center

    Woo, David James

    2016-01-01

    Education systems as units of analysis have been metaphorically likened to ecologies to model change. However, ecological models to date have been ineffective in modelling educational change that is multi-scale and occurs across multiple levels of an education system. Thus, this paper advances two innovative, ecological frameworks that improve on…

  19. Evaluation of the Operational Multi-scale Environment model with Grid Adaptivity (OMEGA) for use in Wind Energy Applications in the Great Basin of Nevada

    NASA Astrophysics Data System (ADS)

    King, Kristien C.

    In order to further assess the wind energy potential for Nevada, the accuracy of a computational meteorological model, the Operational Multi-scale Environment model with Grid Adaptivity (OMEGA), was evaluated by comparing simulation results with data collected from a wind monitoring tower near Tonopah, NV. The state of Nevada is characterized by high mountains and low-lying valleys, therefore, in order to determine the wind potential for the state, meteorological models that predict the wind must be able to accurately represent and account for terrain features and simulate topographic forcing with accuracy. Topographic forcing has a dominant role in the development and modification of mesoscale flows in regions of complex terrain, like Tonopah, especially at the level of wind turbine blade heights (~80 m). Additionally, model factors such as horizontal resolution, terrain database resolution, model physics, time of model initialization, stability regime, and source of initial conditions may each affect the ability of a mesoscale model to forecast winds correctly. The observational tower used for comparison was located at Stone Cabin, Nevada. The tower had both sonic anemometers and cup anemometers installed at heights of 40 m, 60 m, and 80 m above the surface. During a previous experiment, tower data were collected for the period February 9 through March 10, 2007 and compared to model simulations using the MM5 and WRF models at a number of varying horizontal resolutions. In this previous research, neither the MM5 nor the WRF showed a significant improvement in ability to forecast wind speed with increasing horizontal grid resolution. The present research evaluated the ability of OMEGA to reproduce point winds as compared to the observational data from the Stone Cabin Tower at heights of 40 m, 60 m, and 80 m. Unlike other mesoscale atmospheric models, OMEGA incorporates an unstructured triangular adaptive grid which allows for increased flexibility and accuracy in

  20. Multi-scale integrated structural and aeromagnetic analysis to guide tectonic models: An example from the eastern Musgrave Province, Central Australia

    NASA Astrophysics Data System (ADS)

    Aitken, Alan R. A.; Betts, Peter G.

    2009-10-01

    In many polydeformed Precambrian provinces, the understanding of their tectonic history is limited by insufficient exposure, which leads to difficulty in developing links between local and regional architecture, and results in poorly constrained models of their regional-scale architecture. High-resolution aeromagnetic data allows interpretation and modelling at a scale comparable to structural mapping, and by integrating these methods, these links can be developed with high confidence. As an example, we integrate structural mapping, aeromagnetic data interpretation and 3D magnetic inversions in a multi-scale structural analysis of the polydeformed eastern Musgrave Province in central Australia. Deformation during the ca. 1200 Ma Musgravian Orogeny is characterised by an originally northeast-trending structural grain defined by shear zones and tight to isoclinal folds at all scales. 3D magnetic inversion models of syn-to-post Musgravian granites indicate that this structural grain is predominantly west dipping. This architecture suggests that a northeast-oriented fold and thrust belt developed as a result of northwest-southeast compression in central Australia during the Musgravian Orogeny. The next deformation event is characterised by an array of originally east-southeast trending shear zones that truncate and offset the Musgravian structural grain with apparent dextral displacements of up to 1 km. These shear zones are commonly co-located with mafic and granitic dykes, suggesting a dilational origin, and they are interpreted to have initiated under northeast-southwest extension during the ca. 1080 Ma Giles Event. The architecture of these two Mesoproterozoic events was later extensively overprinted by two deformation events during the Pan-African aged (ca. 550 Ma) Petermann Orogeny. The first is characterised by the widespread reactivation of Mesoproterozoic structures, resulting in a network of shear zones of variable orientation, and the second is characterised

  1. A multi-directional and multi-scale roughness filter to detect lineament segments on digital elevation models - analyzing spatial objects in R

    NASA Astrophysics Data System (ADS)

    Baumann, Sebastian; Robl, Jörg; Wendt, Lorenz; Willingshofer, Ernst; Hilberg, Sylke

    2016-04-01

    Automated lineament analysis on remotely sensed data requires two general process steps: The identification of neighboring pixels showing high contrast and the conversion of these domains into lines. The target output is the lineaments' position, extent and orientation. We developed a lineament extraction tool programmed in R using digital elevation models as input data to generate morphological lineaments defined as follows: A morphological lineament represents a zone of high relief roughness, whose length significantly exceeds the width. As relief roughness any deviation from a flat plane, defined by a roughness threshold, is considered. In our novel approach a multi-directional and multi-scale roughness filter uses moving windows of different neighborhood sizes to identify threshold limited rough domains on digital elevation models. Surface roughness is calculated as the vertical elevation difference between the center cell and the different orientated straight lines connecting two edge cells of a neighborhood, divided by the horizontal distance of the edge cells. Thus multiple roughness values depending on the neighborhood sizes and orientations of the edge connecting lines are generated for each cell and their maximum and minimum values are extracted. Thereby negative signs of the roughness parameter represent concave relief structures as valleys, positive signs convex relief structures as ridges. A threshold defines domains of high relief roughness. These domains are thinned to a representative point pattern by a 3x3 neighborhood filter, highlighting maximum and minimum roughness peaks, and representing the center points of lineament segments. The orientation and extent of the lineament segments are calculated within the roughness domains, generating a straight line segment in the direction of least roughness differences. We tested our algorithm on digital elevation models of multiple sources and scales and compared the results visually with shaded relief map

  2. Hands-on, online, and workshop-based K-12 weather and climate education resources from the Center for Multi-scale Modeling of Atmospheric Processes

    NASA Astrophysics Data System (ADS)

    Foster, S. Q.; Johnson, R. M.; Randall, D. A.; Denning, A.; Burt, M. A.; Gardiner, L.; Genyuk, J.; Hatheway, B.; Jones, B.; La Grave, M. L.; Russell, R. M.

    2009-12-01

    The need for improving the representation of cloud processes in climate models has been one of the most important limitations of the reliability of climate-change simulations. Now in its fourth year, the National Science Foundation-funded Center for Multi-scale Modeling of Atmospheric Processes (CMMAP) at Colorado State University (CSU) is addressing this problem through a revolutionary new approach to representing cloud processes on their native scales, including the cloud-scale interaction processes that are active in cloud systems. CMMAP has set ambitious education and human-resource goals to share basic information about the atmosphere, clouds, weather, climate, and modeling with diverse K-12 and public audiences. This is accomplished through collaborations in resource development and dissemination between CMMAP scientists, CSU’s Little Shop of Physics (LSOP) program, and the Windows to the Universe (W2U) program at University Corporation for Atmospheric Research (UCAR). Little Shop of Physics develops new hands on science activities demonstrating basic science concepts fundamental to understanding atmospheric characteristics, weather, and climate. Videos capture demonstrations of children completing these activities which are broadcast to school districts and public television programs. CMMAP and LSOP educators and scientists partner in teaching a summer professional development workshops for teachers at CSU with a semester's worth of college-level content on the basic physics of the atmosphere, weather, climate, climate modeling, and climate change, as well as dozens of LSOP inquiry-based activities suitable for use in classrooms. The W2U project complements these efforts by developing and broadly disseminating new CMMAP-related online content pages, animations, interactives, image galleries, scientists’ biographies, and LSOP videos to K-12 and public audiences. Reaching nearly 20 million users annually, W2U is highly valued as a curriculum enhancement

  3. Multi-scale Measurements and Modeling of Greenhouse Gas and Pollutant Emissions from Coal Power Plants and Gas Mining at Four Corners

    NASA Astrophysics Data System (ADS)

    Dubey, M. K.; Lindenmaier, R.; Henderson, B. G.; Costigan, K. R.; Lee, S.; Herman, J. R.; Love, S. P.; Rahn, T.; Arata, C.; Butterfield, Z.; Chylek, P.; Reisner, J.; Porch, W.

    2012-12-01

    Accurate knowledge of emissions at multiple spatial and temporal scales is indispensable to air quality and climate change research and energy policy. The Four Corners, NM region contains two large coal-fired power plants with real-time in-stack CO2 and pollution monitors making it an ideal site to evaluate top-down verification methods. The air in this region is very polluted and technologies to reduce emissions are being implemented. It also has extensive gas mining with associated fugitive CH4 leaks. We have developed a comprehensive test-bed monitoring site near Farmington, NM that includes a solar Fourier Transform Spectrometer (TCCON) and a solar grating spectrometer (Pandora) to monitor column abundance of greenhouse gases (CO2, CH4, N2O) and pollutants (CO and NO2). We also monitor these trace gases and some isotopes (13CO2 and 13CH4) in situ by cavity ring-down and standard EPA pollution monitors together. In addition we monitor meteorology, boundary layer height and aerosol optical depth. We have made continuous measurements for over 16 months. To interpret our data we have coupled a high-resolution plume model to a nested Weather Research and Forecasting Model with Chemistry. Hourly real-time emissions are taken from in- stack monitors and other spatio-temporally resolved inventories. Our multi-scale forward model simulations are compared with our observations. We report observed power-plant signals, their diurnal cycles, and how they depend on local meteorology. Typically, the total-column in CO2 increases by 2 to 8 ppm when a power-plant plume is blowing towards our site, while the in situ CO2 increases by 10 to 50 ppm. We report the highest columnar measurements of NO2 measured (> 3 DU) and the first remote observations of columnar ratio of NO2/CO2 and 13CO2. Observations of NO2/CO2 and δ13CO2 are used to isolate power plant sources and constrain emissions. In situ CH4 measurements reveal large nocturnal increases of 4 to 5 ppm that could be from

  4. Multi-Scale Change Detection Research of Remotely Sensed Big Data in CyberGIS

    NASA Astrophysics Data System (ADS)

    Xing, J.; Sieber, R.

    2015-12-01

    Big remotely sensed data, the heterogeneity of satellite platforms and file formats along with increasing volumes and velocities, offers new types of analyses. This makes big remotely sensed data a good candidate for CyberGIS, the aim of which is to enable knowledge discovery of big data in the cloud. We apply CyberGIS to feature-based multi-scale land use/cover change (LUCC) detection. There have been attempts to do multi-scale LUCC. However, studies were done with small data and could not consider the mismatch between multi-scale analysis and computational scale. They have yet to consider the possibilities for scalar research across numerous temporal and spatial scales afforded by big data, especially if we want to advance beyond pixel-based analysis and also reduce preprocessing requirements. We create a geospatial cyberinfrastructure (GCI) to handle multi-spatio-temporal scale change detection. We first clarify different meanings of scale in CyberGIS and LUCC to derive a feature scope layer in the GCI based on Stommel modelling. Our analysis layer contains a multi-scale segmentation-based method based on normalized cut image segmentation and wavelet-based image scaling algorithms. Our computer resource utilization layer uses Wang and Armstrong's (2009) method for mainly for memory, I/O and CPU time. Our case is urban-rural change detection in the Greater Montreal Area (5 time periods, 2006-2012, 100 virtual machines), 36,000km2 and varying from 0.6m to 38m resolution. We present a ground truthed accuracy assessment of a change matrix that is composed of 6 feature classes at 12 different spatio-temporal scales, and the performance of the change detection GCI for multi-scale LUCC study. The GCI allows us to extract and coordinate different types of changes by varying spatio-temporal scales from the big imagery datasets.

  5. Multi-scale gravity and cosmology

    SciTech Connect

    Calcagni, Gianluca

    2013-12-01

    The gravitational dynamics and cosmological implications of three classes of recently introduced multi-scale spacetimes (with, respectively, ordinary, weighted and q-derivatives) are discussed. These spacetimes are non-Riemannian: the metric structure is accompanied by an independent measure-differential structure with the characteristics of a multi-fractal, namely, different dimensionality at different scales and, at ultra-short distances, a discrete symmetry known as discrete scale invariance. Under this minimal paradigm, five general features arise: (a) the big-bang singularity can be replaced by a finite bounce, (b) the cosmological constant problem is reinterpreted, since accelerating phases can be mimicked by the change of geometry with the time scale, without invoking a slowly rolling scalar field, (c) the discreteness of geometry at Planckian scales can leave an observable imprint of logarithmic oscillations in cosmological spectra and (d) give rise to an alternative mechanism to inflation or (e) to a fully analytic model of cyclic mild inflation, where near scale invariance of the perturbation spectrum can be produced without strong acceleration. Various properties of the models and exact dynamical solutions are discussed. In particular, the multi-scale geometry with weighted derivatives is shown to be a Weyl integrable spacetime.

  6. Multi-scale modeling study of the source contributions to near-surface ozone and sulfur oxides levels over California during the ARCTAS-CARB period

    NASA Astrophysics Data System (ADS)

    Huang, M.; Carmichael, G. R.; Spak, S. N.; Adhikary, B.; Kulkarni, S.; Cheng, Y.; Wei, C.; Tang, Y.; D'Allura, A.; Wennberg, P. O.; Huey, G. L.; Dibb, J. E.; Jimenez, J. L.; Cubison, M. J.; Weinheimer, A. J.; Kaduwela, A.; Cai, C.; Wong, M.; Pierce, R. Bradley; Al-Saadi, J. A.; Streets, D. G.; Zhang, Q.

    2011-04-01

    Chronic high surface ozone (O3) levels and the increasing sulfur oxides (SOx = SO2+SO4) ambient concentrations over South Coast (SC) and other areas of California (CA) are affected by both local emissions and long-range transport. In this paper, multi-scale tracer, full-chemistry and adjoint simulations using the STEM atmospheric chemistry model are conducted to assess the contribution of local emission sourcesto SC O3 and to evaluate the impacts of transported sulfur and local emissions on the SC sulfur budgetduring the ARCTAS-CARB experiment period in 2008. Sensitivity simulations quantify contributions of biogenic and fire emissions to SC O3 levels. California biogenic and fire emissions contribute 3-4 ppb to near-surface O3 over SC, with larger contributions to other regions in CA. During a long-range transport event from Asia starting from 22 June, high SOx levels (up to ~0.7 ppb of SO2 and ~1.3 ppb of SO4) is observed above ~6 km, but they did not affect CA surface air quality. The elevated SOx observed at 1-4 km is estimated to enhance surface SOx over SC by ~0.25 ppb (upper limit) on ~24 June. The near-surface SOx levels over SC during the flight week are attributed mostly to local emissions. Two anthropogenic SOx emission inventories (EIs) from the California Air Resources Board (CARB) and the US Environmental Protection Agency (EPA) are compared and applied in 60 km and 12 km chemical transport simulations, and the results are compared withobservations. The CARB EI shows improvements over the National Emission Inventory (NEI) by EPA, but generally underestimates surface SC SOx by about a factor of two. Adjoint sensitivity analysis indicated that SO2 levels at 00:00 UTC (17:00 local time) at six SC surface sites were influenced by previous day maritime emissions over the ocean, the terrestrial emissions over nearby urban areas, and by transported SO2 from the north through both terrestrial and maritime areas. Overall maritime emissions contribute 10-70% of

  7. Ecohydrological Linkages, Multi-scale Processes, Temporal Variability, and Drivers of Change in a Degraded Pinyon-Juniper Watershed: Implications for Erosion Modeling

    NASA Astrophysics Data System (ADS)

    Allen, C. D.

    2006-12-01

    In 1993 long-term research began on the runoff and erosion dynamics of a pinyon-juniper woodland hillslope at Bandelier National Monument in northern New Mexico (USA). In the 1.09 ha Frijolito watershed, erosion has been continuously studied at 3 spatial scales: 1 square meter, about 1000 square meters, and the entire watershed. This site is currently representative of degraded woodlands of pinyon (Pinus edulis) and one-seed juniper (Juniperus monosperma) in this region, exhibiting marked connectivity of exposed bare soil interspaces between tree canopy patches and obvious geomorphic signs of accelerated soil erosion (e.g., pedestalling, actively expanding rill networks). Ecological and land use histories show that this site has undergone a number of dramatic ecohydrological shifts since ca. C.E. 1850, transitioning from: 1) open ponderosa pine (Pinus ponderosa) overstory with limited pinyon-juniper component and substantial herbaceous understory that supported surface fires and constrained soil erosion, to; 2) ponderosa pine with reduced herbaceous cover due to livestock grazing after ca.1870, resulting in collapse of the surface fire regime and increased establishment of young pinyon and juniper trees, to; 3) mortality of all of the ponderosa pine during the extreme drought of the 1950s, leaving eroding pinyon-juniper woodland, to; 4) mortality of all mature pinyon at or above sapling size during the 2002-2003 drought, with juniper now the only dominant woody species. Detailed measurements since 1993 document high rates of soil erosion (> 2.75 Mg/ha/year on average at the watershed scale) that are rapidly stripping the local soils. Long-term observations are needed to distinguish short-term variability from longer term trends, as measurements of runoff and erosion show extreme variability at multiple time scales since 1993. The multi-scale erosion data from the Frijolito watershed reveal little dropoff in erosion rate (g/meter-squared) between the one meter

  8. Multi-scale biomedical systems: measurement challenges

    NASA Astrophysics Data System (ADS)

    Summers, R.

    2016-11-01

    Multi-scale biomedical systems are those that represent interactions in materials, sensors, and systems from a holistic perspective. It is possible to view such multi-scale activity using measurement of spatial scale or time scale, though in this paper only the former is considered. The biomedical application paradigm comprises interactions that range from quantum biological phenomena at scales of 10-12 for one individual to epidemiological studies of disease spread in populations that in a pandemic lead to measurement at a scale of 10+7. It is clear that there are measurement challenges at either end of this spatial scale, but those challenges that relate to the use of new technologies that deal with big data and health service delivery at the point of care are also considered. The measurement challenges lead to the use, in many cases, of model-based measurement and the adoption of virtual engineering. It is these measurement challenges that will be uncovered in this paper.

  9. Multi-scale validation of a nanodiamond drug delivery system and multi-scale engineering education

    NASA Astrophysics Data System (ADS)

    Schwalbe, Michelle Kristin

    This dissertation has two primary concerns: (i) evaluating the uncertainty and prediction capabilities of a nanodiamond drug delivery model using Bayesian calibration and bias correction, and (ii) determining conceptual difficulties of multi-scale analysis from an engineering education perspective. A Bayesian uncertainty quantification scheme is used to analyze computational and experimental data for the localized cancer drug delivery system. Since this system is largely unknown, assessing the uncertainty at various developmental stages as well as on different physical scales is important to determine functioning of this system. Adsorption of DOX (a cancer fighting drug) to nanodiamonds is measured in two ways: (1) experimentally via UV Visible Spectroscopy and (2) numerically using stochastic molecular dynamics simulations. These two sets of data are used in a Bayesian calibration and bias correction analysis such that the pH is the input parameter, the percentage of carboxyl, the functional group on the surface of the nanodiamond, is the calibration parameter, and both modeling and experimental errors are accounted for in the uncertainty analysis. The acid dissociating constant pKa value of the nanodiamond is also used for system calibration. A Bayesian bias correction analysis is also performed to measure the impact of nanodiamond aggregation. From these analyses, an estimate of the uncertainty in the system is determined, the optimal pKa value and percentage of carboxyl is found, the impact of the experimental and modeling physical scale differences is examined, the impact of clustering is measured, and a research path to further reducing the system uncertainty is given. The second research issue covered in this dissertation addresses how to effectively teach this type of high-level, cross-disciplinary thinking, and multi-scale research to future engineers. The conceptual hurtles present in understanding multi-scale analysis were identified through one

  10. Air pollution in the Benelux/Rhine-Ruhr area: Numerical simulations with a multi-scale regional chemistry-transport model

    NASA Astrophysics Data System (ADS)

    Memmesheimer, M.; Jakobs, H. J.; Wurzler, S.; Friese, E.; Piekorz, G.; Ebel, A.

    2009-04-01

    The Rhine-Ruhr area is a strongly industrialized region with about 10 Million inhabitants. It is one of the regions in Europe, which has the characteristics of a megacity with respect to population density, traffic, industry and environmental issues. The main centre of European steel production and the biggest inland port of the world is located in Duisburg, one of the major cities in the Rhine-Ruhr area. Together with the nearby urban agglomerations in the Benelux area including Brussels, Amsterdam and in particular Rotterdam as one of the most important sea-harbours of the world together with Singapore and Shanghai, it forms one of the regions in Europe heavily loaded with air pollutants as ozone, NO2 and particulate matter. Ammonia emissions outside the urban agglomerations but within the domain are also on a quite high level due to intense agricultural usage in Benelux, North-Rhine-Westphalia and lower Saxony. Therefore this area acts also as an important source region for gaseous precursors contributing to the formation of secondary particles in the atmosphere. The Benelux/Rhine-Ruhr area therefore has been selected within the framework of the recently established FP7 research project CityZen as one hot spot for detailed investigations of the past and current status of air pollution and its future development on different spatial and temporal scales. Some examples from numerical simulations with the regional multi-scale chemistry transport model EURAD for Central Europe and the Rhine-Ruhr area will be presented. The model calculates the transport, chemical transformations and deposition of trace constituents in the troposphere from the surface up to about 16 km using MM5 as meteorological driver, the RACM-MIM gas-phase chemistry and MADE-SORGAM for the treatment of particulate matter. Horizontal grid sizes are in the range of 100 km down to 1 km for heavily polluted urbanized areas within Benelux/Rhine-Ruhr. The planetary boundary layer is resolved by 15

  11. Advanced modeling to accelerate the scale up of carbon capture technologies

    SciTech Connect

    Miller, David C.; Sun, XIN; Storlie, Curtis B.; Bhattacharyya, Debangsu

    2015-06-01

    In order to help meet the goals of the DOE carbon capture program, the Carbon Capture Simulation Initiative (CCSI) was launched in early 2011 to develop, demonstrate, and deploy advanced computational tools and validated multi-scale models to reduce the time required to develop and scale-up new carbon capture technologies. This article focuses on essential elements related to the development and validation of multi-scale models in order to help minimize risk and maximize learning as new technologies progress from pilot to demonstration scale.

  12. The Adaptive Multi-scale Simulation Infrastructure

    SciTech Connect

    Tobin, William R.

    2015-09-01

    The Adaptive Multi-scale Simulation Infrastructure (AMSI) is a set of libraries and tools developed to support the development, implementation, and execution of general multimodel simulations. Using a minimal set of simulation meta-data AMSI allows for minimally intrusive work to adapt existent single-scale simulations for use in multi-scale simulations. Support for dynamic runtime operations such as single- and multi-scale adaptive properties is a key focus of AMSI. Particular focus has been spent on the development on scale-sensitive load balancing operations to allow single-scale simulations incorporated into a multi-scale simulation using AMSI to use standard load-balancing operations without affecting the integrity of the overall multi-scale simulation.

  13. Viscoelastic Model for Lung Parenchyma for Multi-Scale Modeling of Respiratory System Phase I: Hypo-Elastic Model for CFD Implementation

    SciTech Connect

    Freed, Alan D.; Einstein, Daniel R.

    2011-04-14

    An isotropic constitutive model for the parenchyma of lung has been derived from the theory of hypo-elasticity. The intent is to use it to represent the mechanical response of this soft tissue in sophisticated, computational, fluid-dynamic models of the lung. This demands that the continuum model be accurate, yet simple and effcient. An objective algorithm for its numeric integration is provided. The response of the model is determined for several boundary-value problems whose experiments are used for material characterization. The effective elastic, bulk, and shear moduli, and Poisson’s ratio, as tangent functions, are also derived. The model is characterized against published experimental data for lung. A bridge between this continuum model and a dodecahedral model of alveolar geometry is investigated, with preliminary findings being reported.

  14. A time for multi-scale modeling of anti-fibrotic therapies. Comment on "Towards a unified approach in the modeling of fibrosis: A review with research perspectives" by Martine Ben Amar and Carlo Bianca

    NASA Astrophysics Data System (ADS)

    Wu, Min

    2016-07-01

    The development of anti-fibrotic therapies in diversities of diseases becomes more and more urgent recently, such as in pulmonary, renal and liver fibrosis [1,2], as well as in malignant tumor growths [3]. As reviewed by Ben Amar and Bianca [4], various theoretical, experimental and in-silico models have been developed to understand the fibrosis process, where the implication on therapeutic strategies has also been frequently demonstrated (e.g., [5-7]). In [4], these models are analyzed and sorted according to their approaches, and in the end of [4], a unified multi-scale approach was proposed to understand fibrosis. While one of the major purposes of extensive modeling of fibrosis is to shed light on therapeutic strategies, the theoretical, experimental and in-silico studies of anti-fibrosis therapies should be conducted more intensively.

  15. Multi-Scale 7DOF View Adjustment.

    PubMed

    Cho, Isaac; Li, Jialei; Wartell, Zachary

    2017-02-13

    Multi-scale virtual environments contain geometric details ranging over several orders of magnitude and typically employ out-of-core rendering techniques. When displayed in virtual reality systems this entails using a 7 degree-of-freedom (DOF) view model where view scale is a separate 7th DOF in addition to 6DOF view pose. Dynamic adjustment of this and other view parameters become very important to usability. In this paper, we evaluate how two adjustment techniques interact with uni- and bi-manual 7 degree-of-freedom navigation in DesktopVR and a CAVE. The travel task has two stages, an initial targeted zoom and a detailed geometric inspection. The results show benefits of the auto-adjustments on completion time and stereo fusion issues, but only in certain circumstances. Peculiar view configuration examples show the difficulty of creating robust adjustment rules.

  16. Nonlinear helicons bearing multi-scale structures

    NASA Astrophysics Data System (ADS)

    Abdelhamid, Hamdi M.; Yoshida, Zensho

    2017-02-01

    The helicon waves exhibit varying characters depending on plasma parameters, geometry, and wave numbers. Here, we elucidate an intrinsic multi-scale property embodied by the combination of the dispersive effect and nonlinearity. The extended magnetohydrodynamics model (exMHD) is capable of describing a wide range of parameter space. By using the underlying Hamiltonian structure of exMHD, we construct an exact nonlinear solution, which turns out to be a combination of two distinct modes, the helicon and Trivelpiece-Gould (TG) waves. In the regime of relatively low frequency or high density, however, the combination is made of the TG mode and an ion cyclotron wave (slow wave). The energy partition between these modes is determined by the helicities carried by the wave fields.

  17. APPLICATION OF A NEW LAND-SURFACE, DRY DEPOSITION, AND PBL MODEL IN THE MODELS-3 COMMUNITY MULTI-SCALE AIR QUALITY (CMAQ) MODEL SYSTEM

    EPA Science Inventory

    Like most air quality modeling systems, CMAQ divides the treatment of meteorological and chemical/transport processes into separate models run sequentially. A potential drawback to this approach is that it creates the illusion that these processes are minimally interdependent an...

  18. Bio-inspired homogeneous multi-scale place recognition.

    PubMed

    Chen, Zetao; Lowry, Stephanie; Jacobson, Adam; Hasselmo, Michael E; Milford, Michael

    2015-12-01

    Robotic mapping and localization systems typically operate at either one fixed spatial scale, or over two, combining a local metric map and a global topological map. In contrast, recent high profile discoveries in neuroscience have indicated that animals such as rodents navigate the world using multiple parallel maps, with each map encoding the world at a specific spatial scale. While a number of theoretical-only investigations have hypothesized several possible benefits of such a multi-scale mapping system, no one has comprehensively investigated the potential mapping and place recognition performance benefits for navigating robots in large real world environments, especially using more than two homogeneous map scales. In this paper we present a biologically-inspired multi-scale mapping system mimicking the rodent multi-scale map. Unlike hybrid metric-topological multi-scale robot mapping systems, this new system is homogeneous, distinguishable only by scale, like rodent neural maps. We present methods for training each network to learn and recognize places at a specific spatial scale, and techniques for combining the output from each of these parallel networks. This approach differs from traditional probabilistic robotic methods, where place recognition spatial specificity is passively driven by models of sensor uncertainty. Instead we intentionally create parallel learning systems that learn associations between sensory input and the environment at different spatial scales. We also conduct a systematic series of experiments and parameter studies that determine the effect on performance of using different neural map scaling ratios and different numbers of discrete map scales. The results demonstrate that a multi-scale approach universally improves place recognition performance and is capable of producing better than state of the art performance compared to existing robotic navigation algorithms. We analyze the results and discuss the implications with respect to

  19. Multi-Scale Sizing of Lightweight Multifunctional Spacecraft Structural Components

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.

    2005-01-01

    This document is the final report for the project entitled, "Multi-Scale Sizing of Lightweight Multifunctional Spacecraft Structural Components," funded under the NRA entitled "Cross-Enterprise Technology Development Program" issued by the NASA Office of Space Science in 2000. The project was funded in 2001, and spanned a four year period from March, 2001 to February, 2005. Through enhancements to and synthesis of unique, state of the art structural mechanics and micromechanics analysis software, a new multi-scale tool has been developed that enables design, analysis, and sizing of advance lightweight composite and smart materials and structures from the full vehicle, to the stiffened structure, to the micro (fiber and matrix) scales. The new software tool has broad, cross-cutting value to current and future NASA missions that will rely on advanced composite and smart materials and structures.

  20. Control of Thermo-Acoustics Instabilities: The Multi-Scale Extended Kalman Approach

    NASA Technical Reports Server (NTRS)

    Le, Dzu K.; DeLaat, John C.; Chang, Clarence T.

    2003-01-01

    "Multi-Scale Extended Kalman" (MSEK) is a novel model-based control approach recently found to be effective for suppressing combustion instabilities in gas turbines. A control law formulated in this approach for fuel modulation demonstrated steady suppression of a high-frequency combustion instability (less than 500Hz) in a liquid-fuel combustion test rig under engine-realistic conditions. To make-up for severe transport-delays on control effect, the MSEK controller combines a wavelet -like Multi-Scale analysis and an Extended Kalman Observer to predict the thermo-acoustic states of combustion pressure perturbations. The commanded fuel modulation is composed of a damper action based on the predicted states, and a tones suppression action based on the Multi-Scale estimation of thermal excitations and other transient disturbances. The controller performs automatic adjustments of the gain and phase of these actions to minimize the Time-Scale Averaged Variances of the pressures inside the combustion zone and upstream of the injector. The successful demonstration of Active Combustion Control with this MSEK controller completed an important NASA milestone for the current research in advanced combustion technologies.

  1. PERFORM 60 - Prediction of the effects of radiation for reactor pressure vessel and in-core materials using multi-scale modelling - 60 years foreseen plant lifetime

    NASA Astrophysics Data System (ADS)

    Leclercq, Sylvain; Lidbury, David; Van Dyck, Steven; Moinereau, Dominique; Alamo, Ana; Mazouzi, Abdou Al

    2010-11-01

    In nuclear power plants, materials may undergo degradation due to severe irradiation conditions that may limit their operational life. Utilities that operate these reactors need to quantify the ageing and the potential degradations of some essential structures of the power plant to ensure safe and reliable plant operation. So far, the material databases needed to take account of these degradations in the design and safe operation of installations mainly rely on long-term irradiation programs in test reactors as well as on mechanical or corrosion testing in specialized hot cells. Continuous progress in the physical understanding of the phenomena involved in irradiation damage and continuous progress in computer sciences have now made possible the development of multi-scale numerical tools able to simulate the effects of irradiation on materials microstructure. A first step towards this goal has been successfully reached through the development of the RPV-2 and Toughness Module numerical tools by the scientific community created around the FP6 PERFECT project. These tools allow to simulate irradiation effects on the constitutive behaviour of the reactor pressure vessel low alloy steel, and also on its failure properties. Relying on the existing PERFECT Roadmap, the 4 years Collaborative Project PERFORM 60 has mainly for objective to develop multi-scale tools aimed at predicting the combined effects of irradiation and corrosion on internals (austenitic stainless steels) and also to improve existing ones on RPV (bainitic steels). PERFORM 60 is based on two technical sub-projects: (i) RPV and (ii) internals. In addition to these technical sub-projects, the Users' Group and Training sub-project shall allow representatives of constructors, utilities, research organizations… from Europe, USA and Japan to receive the information and training to get their own appraisal on limits and potentialities of the developed tools. An important effort will also be made to teach young

  2. SENSITIVITY OF OZONE AND AEROSOL PREDICTIONS TO THE TRANSPORT ALGORITHMS IN THE MODELS-3 COMMUNITY MULTI-SCALE AIR QUALITY (CMAQ) MODELING SYSTEM

    EPA Science Inventory

    EPA's Models-3 CMAQ system is intended to provide a community modeling paradigm that allows continuous improvement of the one-atmosphere modeling capability in a unified fashion. CMAQ's modular design promotes incorporation of several sets of science process modules representing ...

  3. Metabolic dynamics in skeletal muscle during acute reduction in blood flow and oxygen supply to mitochondria: in-silico studies using a multi-scale, top-down integrated model.

    PubMed

    Dash, Ranjan K; Li, Yanjun; Kim, Jaeyeon; Beard, Daniel A; Saidel, Gerald M; Cabrera, Marco E

    2008-09-09

    Control mechanisms of cellular metabolism and energetics in skeletal muscle that may become evident in response to physiological stresses such as reduction in blood flow and oxygen supply to mitochondria can be quantitatively understood using a multi-scale computational model. The analysis of dynamic responses from such a model can provide insights into mechanisms of metabolic regulation that may not be evident from experimental studies. For the purpose, a physiologically-based, multi-scale computational model of skeletal muscle cellular metabolism and energetics was developed to describe dynamic responses of key chemical species and reaction fluxes to muscle ischemia. The model, which incorporates key transport and metabolic processes and subcellular compartmentalization, is based on dynamic mass balances of 30 chemical species in both capillary blood and tissue cells (cytosol and mitochondria) domains. The reaction fluxes in cytosol and mitochondria are expressed in terms of a general phenomenological Michaelis-Menten equation involving the compartmentalized energy controller ratios ATP/ADP and NADH/NAD(+). The unknown transport and reaction parameters in the model are estimated simultaneously by minimizing the differences between available in vivo experimental data on muscle ischemia and corresponding model outputs in coupled with the resting linear flux balance constraints using a robust, nonlinear, constrained-based, reduced gradient optimization algorithm. With the optimal parameter values, the model is able to simulate dynamic responses to reduced blood flow and oxygen supply to mitochondria associated with muscle ischemia of several key metabolite concentrations and metabolic fluxes in the subcellular cytosolic and mitochondrial compartments, some that can be measured and others that can not be measured with the current experimental techniques. The model can be applied to test complex hypotheses involving dynamic regulation of cellular metabolism and

  4. [Multi-Scale Convergence of Cold-Land Process Representation in Land-Surface Models, Microwave Remote Sensing, and Field Observations

    NASA Technical Reports Server (NTRS)

    Shi, Jiancheng

    2005-01-01

    The cryosphere is a major component of the hydrosphere and interacts significantly with the global climate system, the geosphere, and the biosphere. Measurement of the amount of water stored in the snow pack and forecasting the rate of melt are thus essential for managing water supply and flood control systems. Snow hydrologists are confronted with the dual problems of estimating both the quantity of water held by seasonal snow packs and time of snow melt. Monitoring these snow parameters is essential for one of the objectives of the Earth Science Enterprise-understanding of the global hydrologic cycle. Measuring spatially distributed snow properties, such as snow water equivalence (SWE) and wetness, from space is a key component for improvement of our understanding of coupled atmosphere-surface processes. Through the GWEC project, we have significantly advanced our understandings and improved modeling capabilities of the microwave signatures in response to snow and underground properties.

  5. Multi-scale modeling of Puget Sound using an unstructured-grid coastal ocean model: from tide flats to estuaries and coastal waters

    SciTech Connect

    Yang, Zhaoqing; Khangaonkar, Tarang

    2010-11-19

    Water circulation in Puget Sound, a large complex estuary system in the Pacific Northwest coastal ocean of the United States, is governed by multiple spatially and temporally varying forcings from tides, atmosphere (wind, heating/cooling, precipitation/evaporation, pressure), and river inflows. In addition, the hydrodynamic response is affected strongly by geomorphic features, such as fjord-like bathymetry and complex shoreline features, resulting in many distinguishing characteristics in its main and sub-basins. To better understand the details of circulation features in Puget Sound and to assist with proposed nearshore restoration actions for improving water quality and the ecological health of Puget Sound, a high-resolution (around 50 m in estuaries and tide flats) hydrodynamic model for the entire Puget Sound was needed. Here, a threedimensional circulation model of Puget Sound using an unstructured-grid finite volume coastal ocean model is presented. The model was constructed with sufficient resolution in the nearshore region to address the complex coastline, multi-tidal channels, and tide flats. Model open boundaries were extended to the entrance of the Strait of Juan de Fuca and the northern end of the Strait of Georgia to account for the influences of ocean water intrusion from the Strait of Juan de Fuca and the Fraser River plume from the Strait of Georgia, respectively. Comparisons of model results, observed data, and associated error statistics for tidal elevation, velocity, temperature, and salinity indicate that the model is capable of simulating the general circulation patterns on the scale of a large estuarine system as well as detailed hydrodynamics in the nearshore tide flats. Tidal characteristics, temperature/salinity stratification, mean circulation, and river plumes in estuaries with tide flats are discussed.

  6. Radiation Damage in Nuclear Fuel for Advanced Burner Reactors: Modeling and Experimental Validation

    SciTech Connect

    Jensen, Niels Gronbech; Asta, Mark; Ozolins, Nigel Browning'Vidvuds; de Walle, Axel van; Wolverton, Christopher

    2011-12-29

    The consortium has completed its existence and we are here highlighting work and accomplishments. As outlined in the proposal, the objective of the work was to advance the theoretical understanding of advanced nuclear fuel materials (oxides) toward a comprehensive modeling strategy that incorporates the different relevant scales involved in radiation damage in oxide fuels. Approaching this we set out to investigate and develop a set of directions: 1) Fission fragment and ion trajectory studies through advanced molecular dynamics methods that allow for statistical multi-scale simulations. This work also includes an investigation of appropriate interatomic force fields useful for the energetic multi-scale phenomena of high energy collisions; 2) Studies of defect and gas bubble formation through electronic structure and Monte Carlo simulations; and 3) an experimental component for the characterization of materials such that comparisons can be obtained between theory and experiment.

  7. A novel method of multi-scale simulation of macro-scale deformation and microstructure evolution on metal forming

    NASA Astrophysics Data System (ADS)

    Huang, Shiquan; Yi, Youping; Li, Pengchuan

    2011-05-01

    In recent years, multi-scale simulation technique of metal forming is gaining significant attention for prediction of the whole deformation process and microstructure evolution of product. The advances of numerical simulation at macro-scale level on metal forming are remarkable and the commercial FEM software, such as Deform2D/3D, has found a wide application in the fields of metal forming. However, the simulation method of multi-scale has little application due to the non-linearity of microstructure evolution during forming and the difficulty of modeling at the micro-scale level. This work deals with the modeling of microstructure evolution and a new method of multi-scale simulation in forging process. The aviation material 7050 aluminum alloy has been used as example for modeling of microstructure evolution. The corresponding thermal simulated experiment has been performed on Gleeble 1500 machine. The tested specimens have been analyzed for modeling of dislocation density, nucleation and growth of recrystallization(DRX). The source program using cellular automaton (CA) method has been developed to simulate the grain nucleation and growth, in which the change of grain topology structure caused by the metal deformation was considered. The physical fields at macro-scale level such as temperature field, stress and strain fields, which can be obtained by commercial software Deform 3D, are coupled with the deformed storage energy at micro-scale level by dislocation model to realize the multi-scale simulation. This method was explained by forging process simulation of the aircraft wheel hub forging. Coupled the results of Deform 3D with CA results, the forging deformation progress and the microstructure evolution at any point of forging could be simulated. For verifying the efficiency of simulation, experiments of aircraft wheel hub forging have been done in the laboratory and the comparison of simulation and experiment result has been discussed in details.

  8. Bridging the PSI Knowledge Gap: A Multi-Scale Approach

    SciTech Connect

    Wirth, Brian D.

    2015-01-08

    Plasma-surface interactions (PSI) pose an immense scientific hurdle in magnetic confinement fusion and our present understanding of PSI in confinement environments is highly inadequate; indeed, a recent Fusion Energy Sciences Advisory Committee report found that 4 out of the 5 top five fusion knowledge gaps were related to PSI. The time is appropriate to develop a concentrated and synergistic science effort that would expand, exploit and integrate the wealth of laboratory ion-beam and plasma research, as well as exciting new computational tools, towards the goal of bridging the PSI knowledge gap. This effort would broadly advance plasma and material sciences, while providing critical knowledge towards progress in fusion PSI. This project involves the development of a Science Center focused on a new approach to PSI science; an approach that both exploits access to state-of-the-art PSI experiments and modeling, as well as confinement devices. The organizing principle is to develop synergistic experimental and modeling tools that treat the truly coupled multi-scale aspect of the PSI issues in confinement devices. This is motivated by the simple observation that while typical lab experiments and models allow independent manipulation of controlling variables, the confinement PSI environment is essentially self-determined with few outside controls. This means that processes that may be treated independently in laboratory experiments, because they involve vastly different physical and time scales, will now affect one another in the confinement environment. Also, lab experiments cannot simultaneously match all exposure conditions found in confinement devices typically forcing a linear extrapolation of lab results. At the same time programmatic limitations prevent confinement experiments alone from answering many key PSI questions. The resolution to this problem is to usefully exploit access to PSI science in lab devices, while retooling our thinking from a linear and de

  9. Collaborating for Multi-Scale Chemical Science

    SciTech Connect

    William H. Green

    2006-07-14

    Advanced model reduction methods were developed and integrated into the CMCS multiscale chemical science simulation software. The new technologies were used to simulate HCCI engines and burner flames with exceptional fidelity.

  10. Multi-scale interactions in Dictyostelium discoideum aggregation

    NASA Astrophysics Data System (ADS)

    Dixon, James A.; Kelty-Stephen, Damian G.

    2012-12-01

    Cellular aggregation is essential for a wide range of phenomena in developmental biology, and a crucial event in the life-cycle of Dictyostelium discoideum. The current manuscript presents an analysis of multi-scale interactions involved in D. discoideum aggregation and non-aggregation events. The multi-scale fractal dimensions of a sequence of microscope images were used to estimate changing structure at different spatial scales. Three regions showing aggregation and three showing non-aggregation were considered. The results showed that both aggregation and non-aggregation regions were strongly multi-fractal. Analyses of the over-time relationships among nine scales of the generalized dimension, D(q), were conducted using vector autoregression and vector error-correction models. Both types of regions showed evidence that across-scale interactions serve to maintain the equilibrium of the system. Aggregation and non-aggregation regions also showed different patterns of effects of individual scales on other scales. Specifically, aggregation regions showed greater effects of both the smallest and largest scales on the smaller scale structures. The results suggest that multi-scale interactions are responsible for maintaining and altering the cellular structures during aggregation.

  11. Advanced Concept Modeling

    NASA Technical Reports Server (NTRS)

    Chaput, Armand; Johns, Zachary; Hodges, Todd; Selfridge, Justin; Bevirt, Joeben; Ahuja, Vivek

    2015-01-01

    Advanced Concepts Modeling software validation, analysis, and design. This was a National Institute of Aerospace contract with a lot of pieces. Efforts ranged from software development and validation for structures and aerodynamics, through flight control development, and aeropropulsive analysis, to UAV piloting services.

  12. Multiscale Modeling of the Deformation of Advanced Ferritic Steels for Generation IV Nuclear Energy

    SciTech Connect

    Nasr M. Ghoniem; Nick Kioussis

    2009-04-18

    The objective of this project is to use the multi-scale modeling of materials (MMM) approach to develop an improved understanding of the effects of neutron irradiation on the mechanical properties of high-temperature structural materials that are being developed or proposed for Gen IV applications. In particular, the research focuses on advanced ferritic/ martensitic steels to enable operation up to 650-700°C, compared to the current 550°C limit on high-temperature steels.

  13. Multi-Scale Approach for Predicting Fish Species Distributions across Coral Reef Seascapes

    PubMed Central

    Pittman, Simon J.; Brown, Kerry A.

    2011-01-01

    Two of the major limitations to effective management of coral reef ecosystems are a lack of information on the spatial distribution of marine species and a paucity of data on the interacting environmental variables that drive distributional patterns. Advances in marine remote sensing, together with the novel integration of landscape ecology and advanced niche modelling techniques provide an unprecedented opportunity to reliably model and map marine species distributions across many kilometres of coral reef ecosystems. We developed a multi-scale approach using three-dimensional seafloor morphology and across-shelf location to predict spatial distributions for five common Caribbean fish species. Seascape topography was quantified from high resolution bathymetry at five spatial scales (5–300 m radii) surrounding fish survey sites. Model performance and map accuracy was assessed for two high performing machine-learning algorithms: Boosted Regression Trees (BRT) and Maximum Entropy Species Distribution Modelling (MaxEnt). The three most important predictors were geographical location across the shelf, followed by a measure of topographic complexity. Predictor contribution differed among species, yet rarely changed across spatial scales. BRT provided ‘outstanding’ model predictions (AUC = >0.9) for three of five fish species. MaxEnt provided ‘outstanding’ model predictions for two of five species, with the remaining three models considered ‘excellent’ (AUC = 0.8–0.9). In contrast, MaxEnt spatial predictions were markedly more accurate (92% map accuracy) than BRT (68% map accuracy). We demonstrate that reliable spatial predictions for a range of key fish species can be achieved by modelling the interaction between the geographical location across the shelf and the topographic heterogeneity of seafloor structure. This multi-scale, analytic approach is an important new cost-effective tool to accurately delineate essential fish habitat and support

  14. Investigation of mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model and experimental optimization/validation

    NASA Astrophysics Data System (ADS)

    Zhang, Le; Qiao, Minna; Gao, Hongjie; Hu, Bin; Tan, Hua; Zhou, Xiaobo; Li, Chang Ming

    2016-08-01

    Herein, we have developed a novel approach to investigate the mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model, experimental optimization of key parameters and experimental data validation of the predictive power of the model. The advantages of this study are that the impact of mechanical stimulation on bone regeneration in a porous biodegradable CaP scaffold is considered, experimental design is used to investigate the optimal combination of growth factors loaded on the porous biodegradable CaP scaffold to promote bone regeneration and the training, testing and analysis of the model are carried out by using experimental data, a data-mining algorithm and related sensitivity analysis. The results reveal that mechanical stimulation has a great impact on bone regeneration in a porous biodegradable CaP scaffold and the optimal combination of growth factors that are encapsulated in nanospheres and loaded into porous biodegradable CaP scaffolds layer-by-layer can effectively promote bone regeneration. Furthermore, the model is robust and able to predict the development of bone regeneration under specified conditions.

  15. Investigation of mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model and experimental optimization/validation.

    PubMed

    Zhang, Le; Qiao, Minna; Gao, Hongjie; Hu, Bin; Tan, Hua; Zhou, Xiaobo; Li, Chang Ming

    2016-08-21

    Herein, we have developed a novel approach to investigate the mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model, experimental optimization of key parameters and experimental data validation of the predictive power of the model. The advantages of this study are that the impact of mechanical stimulation on bone regeneration in a porous biodegradable CaP scaffold is considered, experimental design is used to investigate the optimal combination of growth factors loaded on the porous biodegradable CaP scaffold to promote bone regeneration and the training, testing and analysis of the model are carried out by using experimental data, a data-mining algorithm and related sensitivity analysis. The results reveal that mechanical stimulation has a great impact on bone regeneration in a porous biodegradable CaP scaffold and the optimal combination of growth factors that are encapsulated in nanospheres and loaded into porous biodegradable CaP scaffolds layer-by-layer can effectively promote bone regeneration. Furthermore, the model is robust and able to predict the development of bone regeneration under specified conditions.

  16. Nanostructured particles from multi scale building blocks

    NASA Astrophysics Data System (ADS)

    Hampsey, J. Eric

    Nanotechnology has emerged as one of the most exciting new and developing fields in science today. New nanoscale materials and devices such as nanoparticles, nanocomposites, nanowires, and nanosensors could revolutionize the 21st century in the same way that the transistor and Internet led to the information age. One key component in developing these new technologies is to assemble individual atomic and molecular building blocks into larger structures with fundamentally new properties and functions. Nature is very efficient at assembling multi scale building blocks such as proteins, lipids, and minerals into nanostructured materials such as bone, teeth, diatoms, eggshells, seashells, cell membranes, and DNA. Surfactant and colloidal building block can also be assembled into different nanoscale materials and devices by utilizing hydrophobic/hydrophilic and other surface interactions. Using these concepts, this dissertation focuses on the syntheses and applications of nanostructured particles assembled from multi scale building blocks. Important factors in the synthesis of the particles include particle size, particle morphology, pore size and pore structure. Five different types of nanostructured particles assembled from different multi scale building blocks are demonstrated in this work: (1) Spherical metal/silica mesoporous particles with high surface areas and controllable pore sizes, pore structures, and metal content are synthesized from surfactant, silicate, and metal building blocks for catalytic applications; (2) Mesoporous hollow spheres with controllable pore sizes and pore structures are synthesized from surfactant, silica, and polystyrene building blocks; (3) Spherical mesoporous carbon particles with controllable pore sizes and pore structures are templated from silica particles assembled from silica and surfactant building blocks; (4) Spherical mesoporous, microporous, and bimodal carbon particles are synthesized from sucrose and silica building blocks

  17. Wyoming greater sage-grouse habitat prioritization: a collection of multi-scale seasonal models and geographic information systems land management tools

    USGS Publications Warehouse

    O'Donnell, Michael S.; Aldridge, Cameron L.; Doherty, Kevin E.; Fedy, Bradley C.

    2015-01-01

    We deliver all products described herein as online geographic information system data for visualization and downloading. We outline the data properties for each model and their data inputs, describe the process of selecting appropriate data products for multifarious applications, describe all data products and software, provide newly derived model composites, and discuss how land managers may use the models to inform future sage-grouse studies and potentially refine conservation efforts. The models, software tools, and associated opportunities for novel applications of these products should provide a suite of additional, but not exclusive, tools for assessing Wyoming Greater Sage-grouse habitats, which land managers, conservationists, and scientists can apply to myriad applications.

  18. Air quality forecast of PM10 in Beijing with Community Multi-scale Air Quality Modeling (CMAQ) system: emission and improvement

    NASA Astrophysics Data System (ADS)

    Wu, Q.; Xu, W.; Shi, A.; Li, Y.; Zhao, X.; Wang, Z.; Li, J.; Wang, L.

    2014-10-01

    The MM5-SMOKE-CMAQ model system, which was developed by the United States Environmental Protection Agency (US EPA) as the MODELS-3 system, has been used for daily air quality forecasts in the Beijing Municipal Environmental Monitoring Center (Beijing MEMC), as a part of the Ensemble air quality Modeling forecast System for Beijing (EMS-Beijing) since the 2008 Olympic Games. According to the daily forecast results for the entire duration of 2010, the model shows good performance in the PM10 forecast on most days but clearly underestimates PM10 concentration during some air pollution episodes. A typical air pollution episode from 11-20 January 2010 was chosen, in which the observed air pollution index of particulate matter (PM10-API) reached 180 while the forecast PM10-API was about 100. In this study, three numerical methods are used for model improvement: first, by enhancing the inner domain with 3 km resolution grids, and expanding the coverage from only Beijing to an area including Beijing and its surrounding cities; second, by adding more regional point source emissions located at Baoding, Landfang and Tangshan, to the south and east of Beijing; third, by updating the area source emissions, including the regional area source emissions in Baoding and Tangshan and the local village/town-level area source emissions in Beijing. The last two methods are combined as the updated emissions method. According to the model sensitivity testing results by the CMAQ model, the updated emissions method and expanded model domain method can both improve the model performance separately. But the expanded model domain method has better ability to capture the peak values of PM10 than the updated emissions method due to better reproduction of the pollution transport process in this episode. As a result, the hindcast results ("New(CMAQ)"), which are driven by the updated emissions in the expanded model domain, show a much better model performance in the national standard station

  19. A multi-scale Lattice Boltzmann model for simulating solute transport in 3D X-ray micro-tomography images of aggregated porous materials

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoxian; Crawford, John W.; Flavel, Richard J.; Young, Iain M.

    2016-10-01

    The Lattice Boltzmann (LB) model and X-ray computed tomography (CT) have been increasingly used in combination over the past decade to simulate water flow and chemical transport at pore scale in porous materials. Because of its limitation in resolution and the hierarchical structure of most natural soils, the X-ray CT tomography can only identify pores that are greater than its resolution and treats other pores as solid. As a result, the so-called solid phase in X-ray images may in reality be a grey phase, containing substantial connected pores capable of conducing fluids and solute. Although modified LB models have been developed to simulate fluid flow in such media, models for solute transport are relatively limited. In this paper, we propose a LB model for simulating solute transport in binary soil images containing permeable solid phase. The model is based on the single-relaxation time approach and uses a modified partial bounce-back method to describe the resistance caused by the permeable solid phase to chemical transport. We derive the relationship between the diffusion coefficient and the parameter introduced in the partial bounce-back method, and test the model against analytical solution for movement of a pulse of tracer. We also validate it against classical finite volume method for solute diffusion in a simple 2D image, and then apply the model to a soil image acquired using X-ray tomography at resolution of 30 μm in attempts to analyse how the ability of the solid phase to diffuse solute at micron-scale affects the behaviour of the solute at macro-scale after a volumetric average. Based on the simulated results, we discuss briefly the danger in interpreting experimental results using the continuum model without fully understanding the pore-scale processes, as well as the potential of using pore-scale modelling and tomography to help improve the continuum models.

  20. Multi-scale characterization of nanostructured sodium aluminum hydride

    NASA Astrophysics Data System (ADS)

    NaraseGowda, Shathabish

    instruments were utilized for this work and their data collection and analysis are reported. Quasielastic neutron scattering experiments were conducted at NIST Center for Neutron Research to characterize atomic hydrogen diffusion in bulk and nano-confined NaAlH4. It was observed that upon confinement of NaAlH4, a significantly higher fraction of hydrogen atoms were involved in diffusive motion on the pico-second to nano-second timescales. However, the confinement had no impact on the lattice diffusivities (jump/hopping rates) of atomic hydrogen, indicating that the improved hydrogen release rates were not due to any kinetic destabilization effects. Instead, the investigation strongly suggested thermodynamic destabilization as the major effect of nano-confinement. The local interaction of the metal sites in metal organic frameworks with the infiltrated hydride was studied using extended x-ray absorption spectroscopy technique. The experiments were conducted at Center for Advanced Microstructures and Devices at Louisiana State University. The metal sites were found to be chemically un-altered, hence ruling out any catalytic role in the dehydrogenation at room temperatures. The fractal morphology of NaAlH4 was characterized by ultra-small angle x-ray scattering experiments performed at Argonne National Lab. The studies quantitatively estimated the extent of densification in the course of one desorption cycle. The particle sizes were found to increase two-fold during heat treatment. Also, the nano-confinement procedure was shown to produce dense mass fractals as opposed to pristine NaAlH4, exhibiting a surface fractal morphology. Based on this finding, a new method to identify confined material from un-confined material in nano-composites was developed and is presented. Preliminary results of modeling and correlating multi-scale phenomena using a phase-field approach are also presented as the foundation for future work.

  1. A multi-scale model of dislocation plasticity in α-Fe: Incorporating temperature, strain rate and non-Schmid effects

    SciTech Connect

    Lim, H.; Hale, L. M.; Zimmerman, J. A.; Battaile, C. C.; Weinberger, C. R.

    2015-01-05

    In this study, we develop an atomistically informed crystal plasticity finite element (CP-FE) model for body-centered-cubic (BCC) α-Fe that incorporates non-Schmid stress dependent slip with temperature and strain rate effects. Based on recent insights obtained from atomistic simulations, we propose a new constitutive model that combines a generalized non-Schmid yield law with aspects from a line tension (LT) model for describing activation enthalpy required for the motion of dislocation kinks. Atomistic calculations are conducted to quantify the non-Schmid effects while both experimental data and atomistic simulations are used to assess the temperature and strain rate effects. The parameterized constitutive equation is implemented into a BCC CP-FE model to simulate plastic deformation of single and polycrystalline Fe which is compared with experimental data from the literature. This direct comparison demonstrates that the atomistically informed model accurately captures the effects of crystal orientation, temperature and strain rate on the flow behavior of siangle crystal Fe. Furthermore, our proposed CP-FE model exhibits temperature and strain rate dependent flow and yield surfaces in polycrystalline Fe that deviate from conventional CP-FE models based on Schmid's law.

  2. A multi-scale model of dislocation plasticity in α-Fe: Incorporating temperature, strain rate and non-Schmid effects

    DOE PAGES

    Lim, H.; Hale, L. M.; Zimmerman, J. A.; ...

    2015-01-05

    In this study, we develop an atomistically informed crystal plasticity finite element (CP-FE) model for body-centered-cubic (BCC) α-Fe that incorporates non-Schmid stress dependent slip with temperature and strain rate effects. Based on recent insights obtained from atomistic simulations, we propose a new constitutive model that combines a generalized non-Schmid yield law with aspects from a line tension (LT) model for describing activation enthalpy required for the motion of dislocation kinks. Atomistic calculations are conducted to quantify the non-Schmid effects while both experimental data and atomistic simulations are used to assess the temperature and strain rate effects. The parameterized constitutive equationmore » is implemented into a BCC CP-FE model to simulate plastic deformation of single and polycrystalline Fe which is compared with experimental data from the literature. This direct comparison demonstrates that the atomistically informed model accurately captures the effects of crystal orientation, temperature and strain rate on the flow behavior of siangle crystal Fe. Furthermore, our proposed CP-FE model exhibits temperature and strain rate dependent flow and yield surfaces in polycrystalline Fe that deviate from conventional CP-FE models based on Schmid's law.« less

  3. An Examination of a Multi-Scale Three-Dimensional Variational Data Assimilation Scheme in the Kuroshio Extension Using the Naval Coastal Ocean Model

    DTIC Science & Technology

    2014-01-01

    height , and velocity . The model domain spans longitudes 1371E to 1451E and latitudes 311N to 381N at 3 km horizontal resolution. The model grid has...The y-axis is depth in meters. Fig. 2. Western Pacific region including Japan and Korean Peninsula. Relocatable NCOM model domain within black box...several peaks in the time series of the error metrics. In general the traditional 3DVAR has a higher maximum value (i.e. large errors) than the MS3DVAR

  4. Slow Conduction in the Border Zones of Patchy Fibrosis Stabilizes the Drivers for Atrial Fibrillation: Insights from Multi-Scale Human Atrial Modeling

    PubMed Central

    Morgan, Ross; Colman, Michael A.; Chubb, Henry; Seemann, Gunnar; Aslanidi, Oleg V.

    2016-01-01

    Introduction: The genesis of atrial fibrillation (AF) and success of AF ablation therapy have been strongly linked with atrial fibrosis. Increasing evidence suggests that patient-specific distributions of fibrosis may determine the locations of electrical drivers (rotors) sustaining AF, but the underlying mechanisms are incompletely understood. This study aims to elucidate a missing mechanistic link between patient-specific fibrosis distributions and AF drivers. Methods: 3D atrial models integrated human atrial geometry, rule-based fiber orientation, region-specific electrophysiology, and AF-induced ionic remodeling. A novel detailed model for an atrial fibroblast was developed, and effects of myocyte-fibroblast (M-F) coupling were explored at single-cell, 1D tissue and 3D atria levels. Left atrial LGE MRI datasets from 3 chronic AF patients were segmented to provide the patient-specific distributions of fibrosis. The data was non-linearly registered and mapped to the 3D atria model. Six distinctive fibrosis levels (0–healthy tissue, 5–dense fibrosis) were identified based on LGE MRI intensity and modeled as progressively increasing M-F coupling and decreasing atrial tissue coupling. Uniform 3D atrial model with diffuse (level 2) fibrosis was considered for comparison. Results: In single cells and tissue, the largest effect of atrial M-F coupling was on the myocyte resting membrane potential, leading to partial inactivation of sodium current and reduction of conduction velocity (CV). In the 3D atria, further to the M-F coupling, effects of fibrosis on tissue coupling greatly reduce atrial CV. AF was initiated by fast pacing in each 3D model with either uniform or patient-specific fibrosis. High variation in fibrosis distributions between the models resulted in varying complexity of AF, with several drivers emerging. In the diffuse fibrosis models, waves randomly meandered through the atria, whereas in each the patient-specific models, rotors stabilized in

  5. Multi-Scale Soil Moisture Monitoring and Modeling at ARS Watersheds for NASA's Soil Moisture Active Passive (SMAP) Calibration/Validation Mission

    NASA Astrophysics Data System (ADS)

    Coopersmith, E. J.; Cosh, M. H.

    2014-12-01

    NASA's SMAP satellite, launched in November of 2014, produces estimates of average volumetric soil moisture at 3, 9, and 36-kilometer scales. The calibration and validation process of these estimates requires the generation of an identically-scaled soil moisture product from existing in-situ networks. This can be achieved via the integration of NLDAS precipitation data to perform calibration of models at each ­in-situ gauge. In turn, these models and the gauges' volumetric estimations are used to generate soil moisture estimates at a 500m scale throughout a given test watershed by leveraging, at each location, the gauge-calibrated models deemed most appropriate in terms of proximity, calibration efficacy, soil-textural similarity, and topography. Four ARS watersheds, located in Iowa, Oklahoma, Georgia, and Arizona are employed to demonstrate the utility of this approach. The South Fork watershed in Iowa represents the simplest case - the soil textures and topography are relative constants and the variability of soil moisture is simply tied to the spatial variability of precipitation. The Little Washita watershed in Oklahoma adds soil textural variability (but remains topographically simple), while the Little River watershed in Georgia incorporates topographic classification. Finally, the Walnut Gulch watershed in Arizona adds a dense precipitation network to be employed for even finer-scale modeling estimates. Results suggest RMSE values at or below the 4% volumetric standard adopted for the SMAP mission are attainable over the desired spatial scales via this integration of modeling efforts and existing in-situ networks.

  6. The air quality forecast of PM10 in Beijing with Community Multi-scale Air Quality Modeling (CMAQ) system: emission and improvement

    NASA Astrophysics Data System (ADS)

    Wu, Q.; Xu, W.; Shi, A.; Li, Y.; Zhao, X.; Wang, Z.; Li, J.; Wang, L.

    2014-05-01

    The MM5-SMOKE-CMAQ model system, which was developed by the United States Environmental Protection Agency (US EPA) as the Models-3 system, has been used for daily air quality forecasts in the Beijing Municipal Environmental Monitoring Center (Beijing MEMC), as a part of the Ensemble Air Quality Forecast System for Beijing (EMS-Beijing) since the Olympic Games 2008. According to the daily forecast results for the entire duration of 2010, the model shows good model performances in the PM10 forecast on most days but clearly underestimates some air pollution episodes. A typical air pollution episode from 11-20 January 2010 was chosen, where the observed air pollution index of particulate matter (PM10-API) reached to 180 while the forecast's PM10-API was about 100. In this study, three numerical methods are used for model improvement: first, enhance the inner domain with 3 km resolution grids: the coverage is expanded from only Beijing to the area including Beijing and its surrounding cities; second, add more regional point source emissions located at Baoding, Landfang and Tangshan, which is to the south and east of Beijing; third, update the area source emissions, which includes the regional area source emissions in Baoding and Tangshan and the local village-town level area source emissions in Beijing. As a result, the hindcast shows a much better model performance in the national standard station-averaged PM10-API, whereas the daily hindcast PM10-API reaches 180 and is much closer to the observation and has a correlation coefficient of 0.93. The correlation coefficient of the PM10-API in all Beijing MEMC stations between the hindcast and observation is 0.82, obviously higher than the forecast's 0.54, and the FAC2 increases from 56% in the forecast to 84% in the hindcast, while the NMSE decreases from 0.886 to 0.196. The hindcast also has better model performance in PM10 hourly concentrations during the typical air pollution episode, the correlation coefficient

  7. Experimental validation and effect of modelling assumptions in the hierarchical multi-scale simulation of the cup drawing of AA6016 sheets

    NASA Astrophysics Data System (ADS)

    Ramírez, M. A.; Schouwenaars, R.; Eyckens, P.; Gawad, J.; Kestens, L.; Van Bael, A.; Van Houtte, P.

    2017-01-01

    An essential step in the improvement of design strategies for a wide range of industrial deep drawing applications is the development of methods which allow for the precise prediction of shape and processing parameters. Earlier work has demonstrated, in a clear but qualitative manner, the capabilities of the hierarchical multiscale (HMS) model, which predicts the anisotropic plastic properties of metallic materials based on a statistical analysis of microstructure-based anisotropy and a continuous description of the yield locus. The method is implemented into the ABAQUS finite-element software but, until recently, little attention had been paid to other factors which determine the accuracy of a finite element prediction in general, such as mesh size, friction coefficient and rigid/elastic modelling of the tools. Through the analysis of cup drawing, which is a well-established laboratory-scale test relevant to industrial applications, a quantitative comparison is provided between measured cup geometry and punch force and modelling results for commercial AA6016T4 aluminium sheets. The relatively weak earing behaviour of these materials serves to emphasise the small differences still found between model and experiment, which may be addressed by future refinement of the micromechanical component of the HMS. Average cup height and punch force, which is an important process parameter omitted in earlier studies, depend primarily on the friction coefficient and assumptions in the modelling of the tools. Considering the balance between accuracy and precision, it is concluded that the proposed methodology has matured sufficiently to be used as a design tool at industrial level.

  8. Multi-Scale Dynamics, Control, and Simulation of Granular Spacecraft

    NASA Technical Reports Server (NTRS)

    Quadrelli, Marco B.; Basinger, Scott; Swartzlander, Grover

    2013-01-01

    In this paper, we present some ideas regarding the modeling, dynamics and control aspects of granular spacecraft. Granular spacecraft are complex multibody systems composed of a spatially disordered distribution of a large number of elements, for instance a cloud of grains in orbit. An example of application is a spaceborne observatory for exoplanet imaging, where the primary aperture is a cloud instead of a monolithic aperture. A model is proposed of a multi-scale dynamics of the grains and cloud in orbit, as well as a control approach for cloud shape maintenance and alignment, and preliminary simulation studies are carried out for the representative imaging system.

  9. A Novel Probabilistic Multi-Scale Modeling and Sensing Framework for Fatigue Life Prediction of Aerospace Structures and Materials: DCT Project

    DTIC Science & Technology

    2012-08-25

    energy based crack model has been developed in terms stress fields and dislocation pile-up in crystal plasticity simulations. The second module has...local stresses is found to cause early crack nucleation under dwell fatigue loading in [8]. Fatigue failure in metallic materials due to cyclic loading...growth due to cyclic stresses , and finally coalescence of cracks to cause fast crack propagation. Depending on the material in question, and other

  10. Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute-solvent interactions.

    PubMed

    Štěpánek, Petr; Bouř, Petr

    2014-10-14

    Electronic transitions in the ultraviolet and visible spectral range can reveal a wealth of information about biomolecular geometry and interactions, such as those involved in protein folding. However, the modeling that provides the necessary link between spectral shapes and the structure is often difficult even for seemingly simple systems. To understand as to how conformational equilibria and solute-solvent interaction influence spectral intensities, we collected absorption (UV-vis), electronic circular dichroism (ECD), and magnetic circular dichroism (MCD) spectra of phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp) zwitterions in aqueous solutions, and compared them with quantum-chemical simulations. These aromatic amino acids provide a relatively strong signal in the accessible wavelength range. At the same time, they allow for a relatively accurate modeling. Energies and intensities of spectral bands were reproduced by the time-dependent density functional theory (TD DFT). The solvent was approximated by a continuum as well as clusters containing solvent molecules from the first hydration sphere. The ECD signal was found to be strongly dependent on molecular conformation, and the dependence was much weaker in UV-vis and MCD spectra. All spectral intensities, however, were significantly affected by the solvent approximation; especially for ECD and MCD the usual polarizable continuum solvent model did not yield satisfactory spectral shapes. On the other hand, averaging of the clusters obtained from molecular dynamics simulations provided an unprecedented agreement with the experiment. Proper modeling of the interactions with the environment thus makes the information about the molecular structure, as obtained from the electronic spectra, more accurate and reliable.

  11. Estimating environmental conditions affecting protozoal pathogen removal in surface water wetland systems using a multi-scale, model-based approach.

    PubMed

    Daniels, Miles E; Hogan, Jennifer; Smith, Woutrina A; Oates, Stori C; Miller, Melissa A; Hardin, Dane; Shapiro, Karen; Los Huertos, Marc; Conrad, Patricia A; Dominik, Clare; Watson, Fred G R

    2014-09-15

    Cryptosporidium parvum, Giardia lamblia, and Toxoplasma gondii are waterborne protozoal pathogens distributed worldwide and empirical evidence suggests that wetlands reduce the concentrations of these pathogens under certain environmental conditions. The goal of this study was to evaluate how protozoal removal in surface water is affected by the water temperature, turbidity, salinity, and vegetation cover of wetlands in the Monterey Bay region of California. To examine how protozoal removal was affected by these environmental factors, we conducted observational experiments at three primary spatial scales: settling columns, recirculating wetland mesocosm tanks, and an experimental research wetland (Molera Wetland). Simultaneously, we developed a protozoal transport model for surface water to simulate the settling columns, the mesocosm tanks, and the Molera Wetland. With a high degree of uncertainty expected in the model predictions and field observations, we developed the model within a Bayesian statistical framework. We found protozoal removal increased when water flowed through vegetation, and with higher levels of turbidity, salinity, and temperature. Protozoal removal in surface water was maximized (~0.1 hour(-1)) when flowing through emergent vegetation at 2% cover, and with a vegetation contact time of ~30 minutes compared to the effects of temperature, salinity, and turbidity. Our studies revealed that an increase in vegetated wetland area, with water moving through vegetation, would likely improve regional water quality through the reduction of fecal protozoal pathogen loads.

  12. Multi-scales and multi-satellites estimates of evapotranspiration with a residual energy balance model in the Muzza agricultural district in Northern Italy

    NASA Astrophysics Data System (ADS)

    Corbari, C.; Bissolati, M.; Mancini, M.

    2015-05-01

    Evapotranspiration estimates were performed with a residual energy balance model (REB) over an agricultural area using remote sensing data. REB uses land surface temperature (LST) as main input parameter so that energy fluxes were computed instantaneously at the time of data acquisition. Data from MODIS and SEVIRI sensors were used and downscaling techniques were implemented to improve their spatial resolutions. Energy fluxes at the original spatial resolutions (1000 m for MODIS and 5000 m for SEVIRI) as well as at the downscaled resolutions (250 m for MODIS and 1000 m for SEVIRI) were calculated with the REB model. Ground eddy covariance data and remote sensing information from the Muzza agricultural irrigation district in Italy from 2010 to 2012 gave the opportunity to validate and compare spatially distributed energy fluxes. The model outputs matched quite well ground observations when ground LST data were used, while differences increased when MODIS and SEVIRI LST were used. The spatial analysis revealed significant differences between the two sensors both in term of LST (around 2.8 °C) and of latent heat fluxes with values (around 100 W m-2).

  13. Multi-scale computation methods: Their applications in lithium-ion battery research and development

    NASA Astrophysics Data System (ADS)

    Siqi, Shi; Jian, Gao; Yue, Liu; Yan, Zhao; Qu, Wu; Wangwei, Ju; Chuying, Ouyang; Ruijuan, Xiao

    2016-01-01

    Based upon advances in theoretical algorithms, modeling and simulations, and computer technologies, the rational design of materials, cells, devices, and packs in the field of lithium-ion batteries is being realized incrementally and will at some point trigger a paradigm revolution by combining calculations and experiments linked by a big shared database, enabling accelerated development of the whole industrial chain. Theory and multi-scale modeling and simulation, as supplements to experimental efforts, can help greatly to close some of the current experimental and technological gaps, as well as predict path-independent properties and help to fundamentally understand path-independent performance in multiple spatial and temporal scales. Project supported by the National Natural Science Foundation of China (Grant Nos. 51372228 and 11234013), the National High Technology Research and Development Program of China (Grant No. 2015AA034201), and Shanghai Pujiang Program, China (Grant No. 14PJ1403900).

  14. Multi-scale harmonic model for solar and climate cyclical variation throughout the Holocene based on Jupiter-Saturn tidal frequencies plus the 11-year solar dynamo cycle

    NASA Astrophysics Data System (ADS)

    Scafetta, Nicola

    2012-05-01

    The Schwabe frequency band of the Zurich sunspot record since 1749 is found to be made of three major cycles with periods of about 9.98, 10.9 and 11.86 years. The side frequencies appear to be closely related to the spring tidal period of Jupiter and Saturn (range between 9.5 and 10.5 years, and median 9.93 years) and to the tidal sidereal period of Jupiter (about 11.86 years). The central cycle may be associated to a quasi-11-year solar dynamo cycle that appears to be approximately synchronized to the average of the two planetary frequencies. A simplified harmonic constituent model based on the above two planetary tidal frequencies and on the exact dates of Jupiter and Saturn planetary tidal phases, plus a theoretically deduced 10.87-year central cycle reveals complex quasi-periodic interference/beat patterns. The major beat periods occur at about 115, 61 and 130 years, plus a quasi-millennial large beat cycle around 983 years. We show that equivalent synchronized cycles are found in cosmogenic records used to reconstruct solar activity and in proxy climate records throughout the Holocene (last 12,000 years) up to now. The quasi-secular beat oscillations hindcast reasonably well the known prolonged periods of low solar activity during the last millennium such as the Oort, Wolf, Spörer, Maunder and Dalton minima, as well as the 17 115-year long oscillations found in a detailed temperature reconstruction of the Northern Hemisphere covering the last 2000 years. The millennial three-frequency beat cycle hindcasts equivalent solar and climate cycles for 12,000 years. Finally, the harmonic model herein proposed reconstructs the prolonged solar minima that occurred during 1900-1920 and 1960-1980 and the secular solar maxima around 1870-1890, 1940-1950 and 1995-2005 and a secular upward trending during the 20th century: this modulated trending agrees well with some solar proxy model, with the ACRIM TSI satellite composite and with the global surface temperature

  15. Parcel-scale urban coastal flood mapping: Leveraging the multi-scale CoSMoS model for coastal flood forecasting

    NASA Astrophysics Data System (ADS)

    Gallien, T.; Barnard, P. L.; Sanders, B. F.

    2011-12-01

    California coastal sea levels are projected to rise 1-1.4 meters in the next century and evidence suggests mean tidal range, and consequently, mean high water (MHW) is increasing along portions of Southern California Bight. Furthermore, emerging research indicates wind stress patterns associated with the Pacific Decadal Oscillation (PDO) have suppressed sea level rise rates along the West Coast since 1980, and a reversal in this pattern would result in the resumption of regional sea level rise rates equivalent to or exceeding global mean sea level rise rates, thereby enhancing coastal flooding. Newport Beach is a highly developed, densely populated lowland along the Southern California coast currently subject to episodic flooding from coincident high tides and waves, and the frequency and intensity of flooding is expected to increase with projected future sea levels. Adaptation to elevated sea levels will require flood mapping and forecasting tools that are sensitive to the dominant factors affecting flooding including extreme high tides, waves and flood control infrastructure. Considerable effort has been focused on the development of nowcast and forecast systems including Scripps Institute of Oceanography's Coastal Data Information Program (CDIP) and the USGS Multi-hazard model, the Southern California Coastal Storm Modeling System (CoSMoS). However, fine scale local embayment dynamics and overtopping flows are needed to map unsteady flooding effects in coastal lowlands protected by dunes, levees and seawalls. Here, a recently developed two dimensional Godunov non-linear shallow water solver is coupled to water level and wave forecasts from the CoSMoS model to investigate the roles of tides, waves, sea level changes and flood control infrastructure in accurate flood mapping and forecasting. The results of this study highlight the important roles of topographic data, embayment hydrodynamics, water level uncertainties and critical flood processes required for

  16. Multi-scale validation of a new soil freezing scheme for a land-surface model with physically-based hydrology

    NASA Astrophysics Data System (ADS)

    Gouttevin, I.; Krinner, G.; Ciais, P.; Polcher, J.; Legout, C.

    2012-04-01

    Soil freezing is a major feature of boreal regions with substantial impact on climate. The present paper describes the implementation of the thermal and hydrological effects of soil freezing in the land surface model ORCHIDEE, which includes a physical description of continental hydrology. The new soil freezing scheme is evaluated against analytical solutions and in-situ observations at a variety of scales in order to test its numerical robustness, explore its sensitivity to parameterization choices and confront its performance to field measurements at typical application scales. Our soil freezing model exhibits a low sensitivity to the vertical discretization for spatial steps in the range of a few millimetres to a few centimetres. It is however sensitive to the temperature interval around the freezing point where phas